# Patent

## Title
Systems and methods for rational selection of context sequences and sequence templates

## Abstract

Provided are systems and methods for rational selection of context sequences and sequence templates including a computer implemented method for obtaining a repository of attributes sets where the attributes sets are statistically associated with a sequence template representing two or more context sequences.

## Background
This Application is a Continuation Application of U.S. patent application Ser. No. 12/733,256 filed on Feb. 19, 2010, which is a 371 of International Application No. PCT/IL2008/001140 filed on Aug. 20, 2008, which claims benefit from U.S. Provisional Patent Application No. 60/935,592 under 35 U.S.C. 119(e) filed on Aug. 21, 2007, the entire content of each of which is hereby incorporated by reference in its entirety.


FIELD OF INVENTION
The present invention relates to the analysis of polynucleotide sequence clusters, and in particular for the characterization of such sequence according to one or more parameters.
BACKGROUND OF THE INVENTION
I. Analyzing Polynucleotide Sequences by Clustering
The increasing amounts of polynucleotide sequence data present an analytical challenge. Such large amounts of data on the one hand provide an opportunity for extensive research, but on the other hand are difficult to analyze by conventional analytical methods. However, one method that has been found to be generally effective for analyzing such large amounts of sequence data is clustering.
Clustering may be performed in a variety of methods. Hierarchical clustering, for example, seeks to create by steps of either mergers or divisions, a hierarchy of segments or clusters. Agglomerative approaches build the hierarchy of clusters by steps of such mergers. Some approaches combine the above two1.
In addition, there are also non-hierarchical methods, which do not seek to create a hierarchy of segments or clusters. The K-Means clustering algorithm is an example of such a clustering technique. It has been used in combination with other techniques, for example, for exploring protein structure2. It was also used to identify recurring local sequence motifs for proteins3.
II. Context Polynucleotide Sequence Analysis
Heidecker and Messing4 found the NNANNAUGGC (SEQ ID NO:1) motif in the AUG context. Joshi5 identified the consensus sequence of AAAAACAA[A/C]AAUGGC (SEQ ID NO:2).
More recently, a survey which included 5074 plant genes demonstrated that higher plants have an AC-rich consensus sequence, aaaaacaA(A/C)aAUGGCg (SEQ ID NO:3)as a context of AUG6. These finding were recently supported7.
Analysis of 5′ untranslated region of mRNA of vertebrates were initially focused on conserved consensus sequence signals which accommodated translation initiation8. Studies which followed, attempted to analyze the consensus sequence about said translation initiation signal9. The later study has demonstrated conserved purines at position −3 and at position +4. The following conserved sequences were identified in the same study: (GCC)GCC(A/G)CCAUGG (SEQ ID NO:4).
Consensus sequences are useful in research for locating the translation initiator codon. The untranslated leader sequence may additionally influence gene expression levels10. It was previously appreciated that Kozak-Like elements in the context of the initiator codon indeed affect expression levels11,12,13,14. Therefore, in U.S. Pat. No. 7,253,342, leader sequence was used to directly influence the expression of the specifically attached gene by either increasing expression, or for maintaining stable mRNA levels15.
SUMMARY OF THE INVENTION
In one aspect, the present invention is directed to a computer implemented method for obtaining a repository of attributes sets, wherein attributes sets are statistically associated with a sequence template representing two or more context sequences, comprising:
(a) obtaining a dataset of context sequences;
(b) transforming each context sequence to a sequence template, thereby obtaining a dataset of sequence templates;
(c) clustering said dataset of sequence templates into a plurality of clusters according to a distance formula; wherein at least one of said clusters is statistically associated with at least one attributes set;
(d) inserting into said repository each of said clusters and said attributes set
which is statistically associated with said each of said clusters;
In one embodiment, the dataset of context sequences of step is further subjected to multiple sequence alignment. The later provides a solution in a particular instance, for example, where the context sequences in the data set are of different lengths or where the context sequences in the data were substantially affected by insertion/deletion regions.
In another aspect, the present invention is directed to repository obtained by the computer implemented method obtaining a repository of attributes sets as defined.
In a second aspect, the present invention is directed to a computer implemented method for identifying a sequence template as statistically associated with an attributes set of interest, comprising:
(a) providing a repository of attributes sets; wherein attributes sets are statistically associated with a sequence template representing two or more context sequences;
(b) selecting an attributes set; and
(c) retrieving at least one sequence template statistically associated with said attributes set.
Optionally, the computer implemented for identifying a sequence template as statistically associated with an attributes set of interest, further comprises the step of merging at least two retrieved sequence templates.
In one embodiment, the attributes are selected from: the Gene Ontology Project (GO), Interpro annotation (European Molecular Biology Laboratory, EMBL), SMART (a Simple Modular Architecture Research Tool, found at (smart.embl-heidelberg.de, UniProt Knowledgebase (SwissProt), OMIM (by NCBI) PROSITE (by the Swiss Institute of Bioinformatics), Protein Information Resource (PER), GeneCards, and Kyoto Encyclopedia of Genes and Genomes (KEGG).
In a third aspect, the present invention is directed to a computer memory system comprising a plurality of tree topologies representing plurality of (k) heaps, wherein the plurality of tree topologies is managed through a common interface; and (k≧1).
In a one embodiment, the heaps are min heaps. In another embodiment, the heaps are max heaps.
In yet another embodiment, an active subset of heaps is held in Random Access Memory (RAM), while the rest of said heaps are maintained on a secondary storage.
In yet another aspect, the invention is directed to a computer implemented method for clustering a plurality of polynucleotide sequences, comprising: determining an attributes set for the plurality of polynucleotide sequences; and clustering the polynucleotide sequences into a plurality of clusters according to values of said attributes set.
In another aspect, the invention is further directed to a method of preparing a polynucleotide construct, comprising:
(a) identifying a sequence template as statistically associated with an attributes set of interest according to the method of the present invention;
(b) preparing a polynucleotide construct having at least one portion operably linked to a context sequence; wherein said context sequence is characterized as having either 80%-85%, 85%-90%, or 90%-100% homology with said sequence template.
In another embodiment, the preparing step comprises synthesizing said context sequence. In another embodiment, the preparing step comprises the preparing of an expression vector comprising said context sequence. In another embodiment, the preparing step comprises the preparing of a probe comprising said context sequence.
In another aspect, the present invention is directed to a computerized system configured for identifying a sequence template as statistically associated with an attributes set of interest, the computerized system comprising: context sequence clustering module, configured to cluster said sequences into a plurality of clusters; an enrichment analysis module, configured to provide enrichment appraisal, wherein context sequence clustering module being communicatively coupled to the enrichment analysis module.
Unless otherwise defined, all technical and scientific terms used herein have the same meaning as commonly understood by one of ordinary skill in the art to which this invention belongs. The materials, methods, and examples provided herein are illustrative only and not intended to be limiting.
Although the present invention is described with regard to a “computer” which may optionally be implemented on a “computer network”, it should be noted that optionally any device featuring a data processor and/or the ability to execute one or more instructions may be described as a computer, including but not limited to a PC (personal computer), or a server. Any two or more of such devices in communication with each other, and/or any computer in communication with any other computer may optionally comprise a “computer network”.



BRIEF DESCRIPTION OF THE DRAWINGS
The present invention is illustrated by way of example, and not by way of limitation, in the figures of the accompanying drawings and in which like reference numerals refer to similar elements and in which:
FIG. 1 illustrates, in accordance with one embodiment of the present invention, an exemplary computerized system on which the present invention may be implemented.
FIG. 2a illustrates, in accordance with one embodiment of the present invention, an exemplary user interface for obtaining a requested function array from a user.
FIG. 2b illustrates, in accordance with one embodiment of the present invention, an exemplary user interface for obtaining a function array or attributes set of interest which is optionally provided by a user.
FIG. 3 illustrates, in accordance with one embodiment of the present invention, an exemplary user interface for proposing the predicted context sequences for synthesis. Among the nucleotide sequences shown are GCCCGNCCGCC (SEQ ID NO:5) and TGCCGCCGCC (SEQ ID NO:6).
FIG. 4 illustrates, in accordance with one embodiment of the present invention, an exemplary viewer application reproducing a context sequence, the cellular function annotations and the size of the context sequence cluster.
FIG. 5 illustrates, in accordance with one embodiment of the present invention, an exemplary data structure of a function attribute array or the cellular function annotations array.
FIG. 6 illustrates, in accordance with one embodiment of the present invention, a simplified example of ascertaining the processing order of templates. (a) and (b) are two clusters of templates having equal minimum distances to a common template.
FIG. 7 illustrates, in accordance with one embodiment of the present invention, a Simplified example of ascertaining the processing order of clusters. (a′) is a new cluster representing a merger of closest neighbors of (a) which was shown in FIG. 6, and (b) is to be handled subsequently.
FIG. 8 illustrates, in accordance with one embodiment of the present invention, a multiple-tree-array topology within a memory module. The top item is defined as the element having the minimal key value amongst the (k) specific min heaps as shown.
FIG. 8a illustrates, in accordance with one embodiment of the present invention, a multiple-tree-array topology within a memory module. The top item is defined as the element having the maximal key value amongst the (k) specific heaps as shown.



DETAILED DESCRIPTION OF THE INVENTION
The present invention, in some embodiments, is of a system and method for analyzing a plurality of nucleotide or other sequences. In other embodiments, the present invention relates to a system and method which provide more efficient memory structures and computational processes. The later system and method may optionally be used with the former embodiments or may optionally be used independently.
For the sake of clarity only and without any intention of being limiting, the below description is divided into three sections. Section I relates to the system of the present invention; Section II relates to embodiment for obtaining of a repository of attributes sets, statistically associated with context sequences and/or a sequence template representing the them; Section III relates to embodiments which provide more efficient memory structures and computational processes; Section IV details embodiments of a computer implemented method for identifying a sequence template as statistically associated with an attributes set of interest; and Section V relates to experimental examples using such embodiments;
Nomenclature
For the purposes of the present invention, “cellular function annotation”, “function attribute”, and “attribute” of a given gene shall mean an attribute, term, characterization, molecular function annotation, or biological process annotation describing a gene or a gene product. The terms can be used interchangeably and synonymously herein. The cellular function annotation are typically reported in variety of sources such as, but not limited to, the Gene Ontology Project (GO), Interpro annotation (European Molecular Biology Laboratory, EMBL), SMART (a Simple Modular Architecture Research Tool, found at (smart.embl-heidelberg.de), UniProt Knowledgebase (SwissProt), OMIM (by NCBI) PROSITE (by the Swiss Institute of Bioinformatics), Protein Information Resource (PIR), GeneCards, Kyoto Encyclopedia of Genes and Genomes (KEGG). It should be emphasized that the above terms and attributes are continuously updated, and new versions are made available on a monthly basis and therefore the systems and methods of the present invention should be interpreted as limited by the gene annotation known at time of filing the application for the invention. Furthermore, it should be noted that the user may optionally operate the method or system of the present invention with any such function attributes, as long as they may be characterized according to a numerical grade; such a grade may optionally be Boolean (“1” or “0”), or alternatively may feature a plurality of discrete numbers or continuous numerical values.
By way of an illustrative example, the term or attribute “cell adhesion” associated to Homo sapiens discoidin domain receptor tyrosine kinase 1 (DDR1, RefSeq accession: NM_001954) is a cellular function annotation. This attribute is found, for example, in Gene Ontology under GO:0007155.
The term “complete function attributes set”, and “complete attributes set” shall mean the complete set of function attributes i.e. all function attributes stored in a repository of the present invention. The terms can be used interchangeably and synonymously herein.
The term “function attributes set”, “attributes set” and “function attributes array” shall mean a subset of the complete function attributes set. The terms can be used interchangeably and synonymously herein. Optionally, the function attributes array can be used to represent a specific user selection in which the user manifests particular function attributes of interest. The user can typically select an attributes set in order to perform the computer implemented method of the present invention for identifying a sequence template whish is statistically associated with the attributes set of interest.
Alternatively, by way of non-limiting example, the attributes set can be used to represent attributes set which is statistically associated with a sequence template. The later can be identified in functional appraisal performed by the methods and system of the present invention. The later is typically performed with respect to a cluster of context sequences or attributes associated with a gene operably linked to the context sequences of the cluster. The results of the functional appraisal performed can thus be represented by an attributes set.
The attributes set optionally feature an array of real numbers, with each of said numbers representing a level of association of a particular annotation or attribute. It can also feature an array of binary digits, where each of said binary digit representing association with a particular annotation or attribute. In this case, ‘0’ can represent the absence of association of a particular function attribute and ‘1’ can indicates statistical association of the particular function attribute.
The term “sequence” shall mean a polynucleotide sequence, continuous or otherwise, of nucleotides being selected from a group consisting of deoxyribonucleotides (DNA) and ribonucleotides (RNA), genomic or otherwise, coding or non-coding. Sequence does not encompass therefore gene order in general or genomic meta structures.
The term “context sequence” shall mean a sequence which regulate or affect a gene product (mRNA, polypeptide and alike). Context sequences consist of at least portion of un-translated sequence. By way of non-limiting example, a context sequence may comprise a sequence which is operably linked to a coding region, sequence affecting expression level of a gene product or otherwise a sequence regulating gene product (or activity). Therefore, a context sequence may comprise a stretch of nucleotides preceding the translation initiation codon of mRNA molecule. A context sequence may comprise a stretch of nucleotides downstream to the translation termination codon of mRNA molecule. In the above examples the context sequence was defined by its relative location to a coding region. However, a context sequence of the present invention may further comprise a promoter, enhancer, inhibitor or other regulatory region.
For the purposes of the present invention, “template” or “sequence template” shall include a matrix T4×l, where (l) denotes the length of the context sequences or aligned context sequence which are represented by the template. The template can either represent the distribution of each nucleotide for each position along a context sequence. The template can further include a matrix (T) where T[a,i] holds the distribution of nucleotide (a) at position (i) in of the context sequences represented. The terms can be used interchangeably and synonymously herein.
As discussed below, at initiation of a clustering method each context sequence is transformed to a template. The skilled person in the art would appreciate that context sequence transformation into a template can typically be performed as an integral part of matrix allocation. By way of a non-limiting example, if a single context sequence has ‘A’ at position 3 then T[‘A’,3]=1.0 (T[‘C’,3]=0, for obvious reasons).
For example, the sequence ‘AG’ is represented by a template having the following distribution matrix:
Simplified example of distribution matrix held in a template, at initialization. At this stage, the template represents a single sequence having the prescribed distributions.














Position = 0
Position = 1




















P(A)
1.0
0



P(G)
0
1.0



P(T)
0
0



P(C)
0
0










During the prosecution of the methods of the present invention a sequence template can represent a cluster of context sequences and the distribution matrix will thus reflect the distribution of nucleotides which characterizes the context sequences within the cluster. The sequence template can typically further comprise a set of gene names or unique identifiers which are operably linked or affected by the context sequences represented thereby.
The term “repository” and “database” shall mean a database or any system configured for insertion and retrieval of information of the present invention. The terms can be used interchangeably and synonymously herein.
The repository of the present invention is typically configured for insertion and retrieval of attributes, attributes set, and context sequences. The later are typically in a form of sequence of ASCII characters. The repository of the present invention can also be configured for insertion and retrieval of sequence templates which can typically comprise an array of numbers, or a 2D matrix of numbers. Moreover, a repository of the present invention is typically configured to insert and retrieve pointers or association between information elements stored therein. In particular, the repository of the present invention can insert and retrieve an attributes set, a sequence template, and to associate between them; so as to enable retrieval of a sequence template together with at least one respective attributes set. Moreover, it can be configured to enable retrieval of an attributes set together with at least one respective sequence template.
The term “multiple sequence alignment”, “MSA” or “alignment” shall have the ordinary meaning as used by the skill person in the art of bioinformatics. CLUSTAL W is typical software package used for that purpose, and can be utilized by usage of default values and other values being adapted for the particular dataset in hand.
The term “synthetic context sequence” or “predicted context sequence” shall mean at least one context sequence or sequence template representing said context sequence that was identified by the systems and methods of the present invention, as statistically associated with an attributes set of interest.
Embodiments of the invention can be used in a general purpose computer system suitably adapted and designed for performing the extensive context sequences clustering, enrichment analysis and comparison.
Section I
FIG. 1 illustrates, in accordance with one embodiment of the present invention, an exemplary system on which the present invention may be implemented. In an embodiment, the computerized system 100 permits clients or users to provide an attributes set of interest for analysis 135. Typically, the attributes set can consist of two or more attributes of interest.
The clients or users can further provide a dataset of context sequences 105 as input information; thereby obtaining a dataset of context sequences for analysis. The context sequences can typically further comprise a set of gene names or unique identifiers which are operably linked or affected by the context sequences, respectively. The attributes set of interest 135 and context sequences 105 can be entered via a user interface specifically configured for that purpose. Where the system 100 is implemented on a computer network, the attributes set 135 and context sequences 105 can be provided through a browser application, such as, but not limited to web browsing application. Alternatively, the attributes set 135 or the context sequences 105 can be comprised in a file. The file can be uploaded to the system 100 though either a network or other information uploading methods known in the art for that purpose.
The context sequence clustering module 110 clusters the context sequences as described hereinafter. Typically, the dataset of context sequences 105 comprises a huge amount of sequence information. In turn, each context sequence is transformed into a sequence template. Clustering of the dataset of sequence templates is performed and results with plurality of clusters. In turn, each gene cluster or the genes which are regulated or affected by the context sequences within the cluster, is subjected to functional appraisal. The result of the functional appraisals is a plurality of clusters each statistically associated with their respective attributes set. The system and method of the present invention enables obtaining of heterogeneous clusters, as defined below.
The clustering procedures of the present invention are, inter alia, utilized in order to obtain a repository of attributes sets, statistically associated with a sequence template. Optionally, the sequence template represents two of more context sequences. The later may not be identical. Therefore, the clustering procedures of the present invention enable obtaining a heterogeneous repository, as defined hereinafter.
The clustering procedures of the present invention can use a 2-dimensional distance matrix to store and retrieve distance related information. However, in order to produce improved performance, distance related information is typically stored and retrieved from computer memory system comprising of plurality of heaps 130, or heap data structures. Data items which are stored and retrieved in the computer memory system 130 of the present invention typically comprise references pointing at two matrixes or templates and a real number. Each said templates represent a cluster of context sequences and the real number measures the distance between the clusters. Optionally, data items may further comprise information such as, but not limited to, gene names or unique identifiers of genes which were classified within the clusters. Alternatively, a template can further comprise information such as gene names or unique identifiers genes which were classified within the cluster which is represented by the template.
Clustering of the present invention is typically performed by the clustering module 110. The context sequence clustering module 110 stores and retrieves data items from the computer memory system (or memory module) 130. The structure of the computer memory system is described below. In essence, the memory system is based on plurality of Heap data structure which was restructured and remodeled, as described below, to improve performance especially where large data set are in hand. For the purpose of the present application, the memory systems shall also be referred to as “multiple-tree-array” the particulars of which are described below. The later typically comprises min heaps and adheres to the invariant according to which the top data item in the multiple-tree-array is a data item referencing a pair of templates having a minimal distance between them. The multiple-tree-array allows the system 100 to perform the clustering of the context sequences and enrichment analysis at an extremely efficient manner reducing the complexity by about one order in comparison to typical 2-dimensional distance matrixes.
The enrichment analysis module 120 performs enrichment appraisals or functional appraisals as described below. In an embodiment, the context sequence clustering module 110 sends a request to the enrichment analysis module 120. The request comprises a data set of context sequences or unique identifiers representing the context sequences within a cluster or unique identifiers of genes regulated or otherwise affected by context sequences. The request typically channeled through either a communication port, BUS or a computer network 115 to the enrichment analysis module 120.
In an embodiment, clusters of context sequences together with their respective enrichment appraisals can be stored in or retrieved from a repository or database 125. In an embodiment, the results of enrichment appraisals are represented by an attributes set or function attribute array being associated with respective cluster or clusters.
The function array comparator 140 is adapted to compare the attributes set of interest (typically provided by a user), with said stored enrichment appraisals retrieved from the repository 125.
FIG. 2a and FIG. 2b illustrate, in accordance with one embodiment of the present invention, an exemplary user interface 200 for obtaining an attributes set of interest from a user. As an alternative, an attributes set is obtained from a client over the network (not shown). The client may be local or remote, either human or automated procedure performed on a computer system. Typically, the user select an attributes set from a list of function attributes 210. The list of function attributes contains at least a sub set of a complete function attributes set. In one embodiment, the user selects the function attributes of interest in order retrieve a sequence template statistically associated with his selection.
The sequence template retrieved can be used in order to design a context sequence for the purpose of either synthesis or manufacture of polynucleotide construct, or vector. In a one embodiment, the context sequence designed comprises the most dominant nucleotide in each position along the sequence template retrieved. In another embodiment, the context sequence designed comprises 80%-85%, 85%-90%, or 90%-100% homology with sequence template or the sequence comprising the most dominant nucleotide in each position along the sequence template.
The subset of function attributes selected by the user can be represented by a function attribute array or the attributes set. The manual selection can be performed with checkboxes 215 which indicate whether a particular function attribute was selected. As the complete function attributes set stored in the computerized system 100 may exceed the page size, page scroller 205 can provide means for navigating through the entire list of function attribute. The list of function attributes can be organized by several techniques, such as but not limited to, lexicographical order, classification, or source of the function attribute. In another embodiment, the user interface includes textboxes 220 in which a user enters the importance degree or confidence level associate with a particular function attribute.
The system of the present invention is adapted to retrieve an enrichment appraisal previously stored in the repository. The enrichment appraisal typically shares a similarity with an attributes set of interest. In another embodiment, the system of the present invention is adapted to retrieve an enrichment appraisal which shares similarity with an attributes set of interest at a predetermined threshold. Alternatively, the system of the present invention is adapted to retrieve an enrichment appraisal which shares maximal similarity with an attributes set of interest.
The output 150 comprises a cluster of context sequences or a sequence template representation thereof, which is statistically associated with said retrieved enrichment appraisal(s). In an embodiment, the output 150 comprises a cluster of context sequences or sequence template representation thereof which are statistically associated with said retrieved enrichment appraisal(s).
Those skilled in the art would appreciate that the invention may be practiced with other computer based system configurations, including network PCs, or hardware specifically designed to perform the procedures and functionalities contemplated hereinafter. The invention may also be practiced in distributed computing environments where procedure of the present invention is performed by remote dedicated processing devices that are linked through a communications network. In a distributed computing environment, for example, program modules such as 110, 120, 125, 130, and 140 may be located in both local and remote apparatus.
The components shown in FIG. 1 are only examples, and are not intended to suggest any limitation as to the scope of the functionality of the invention; the invention is not necessarily dependent on the features shown in FIG. 1.
FIG. 3 illustrates, in accordance with one embodiment of the present invention, an exemplary user interface 300 providing an identified context sequence 310 or a sequence template representing a cluster of context sequences statistically associated with the attributes set of interest. Typically, the identified context sequence or the sequence template consists of those which are statistically associated with stored attributes sets sharing maximal similarity with the attributes set of interest. Similarity or similarity degree is determined by the method described below.
In an embodiment, the user interface 300 includes a textbox, label, or information box 320. Each context sequence 310 or sequence template (not shown) can be associated with textbox, label, or information box 320. The textbox, label, or information box may include statistical confidence level of the context sequence such as p_value or a false discovery rate (FDR) or other enrichment estimator. The page scroller 305 can provide means for navigating through the entire list of context sequences where, for example, the predicted context sequences exceed the window size of the user interface 300.
FIG. 4 illustrates, in accordance with one embodiment of the present invention, another exemplary user interface 400 consists of a sequence template 410 representing a cluster of context sequences, said statistically associated attributes set 420 and the size of the cluster 430. Typically, the user interface 400 can be reached be double clicking on a predicted context sequences 310. The distribution table 415 can comprises a matrix representing the probability of a given nucleotide at a particular position along the context sequences of the current cluster viewed. Each column can represent a position along a predicted context sequence. The most dominant nucleotide at a particular position along the identified context sequences can appear at the top of the respective column 410. Where two nucleotides share similar of identical dominance level both can appear at the top of the respective column 425.
In another embodiment, the user interface 400 is utilized for viewing the clustered context sequences 410 comprising polypeptide sequences. In such an embodiment, the distribution table 415 can comprise a matrix representing the probability of a given amino acid at a particular position along the predicted context sequence. Each column can represent a position along a predicted context sequence. The most dominant amino acid at a particular position along the predicted context sequence can appear at the top of the respective column 410, while two amino acids sharing similar or identical dominance levels both can appear at the top of the respective column 425.
FIG. 5 illustrates, in accordance with one embodiment of the present invention, an exemplary data structure of a function attribute array or the attributes set 500. The attributes set 500 typically features a matrix of cells or items 510. Each of the cells in the matrix can comprise several fields or objects. In an embodiment, the first field of object is a function name/attribute 520 and the second is a value 530 associated therewith. The value 530 may optionally represent a Boolean variable. In an embodiment, where a Boolean variable in a cell holds #true, for example 530, the attributes set includes the particular attribute 520. On the other hand, where a Boolean variable in a cell holds #false the attributes set does not include the particular attribute. In another embodiment, value 530 can be represented a Real variable which represents the statistical confidence level of the particular attribute. By way of non-limiting example, where value 530 hold “1.0E-17”, the function attribute array highly likely to include a particular attribute 520. On the other hand, if value 530 hold “1.0”, the function attribute array most likely does not include the particular attribute 520.
One of ordinary skill in the art would appreciate that the data structure of the attributes set can be varied almost indefinitely. Many other data structures can be employed for storing a subset of attribute. By way of non limiting examples, the attributes set may optionally be stored as a Dictionary or hash table. Other one limiting examples: array of pair <string, boolean>, or indeed a 2D matrix where one dimension is the function attribute and the other dimension is a value.
The attributes set of interest 135 can be represented by the function attribute array 500.
As a mere illustration of the functionality of the present invention, the user may seek to identify one or more sequence templates associated with an attributes set of interest. Assume that the user wishes to consider immunoglobulin and transcription regulation with respect to humans. The user selection of interest is transformed into an attributes set 135 which are typically represented by the function attribute array 500. The function array comparator 140 compares the attributes set received comprising the user selection with said stored enrichment appraisals. The later are retrieved from the repository 125, with respect to humans. Typically, the user can request retrieval of a stored sequence template which is statistically associated with the specific function attributes chosen by the user. Alternatively, the user can retrieve the context sequences which were clustered together, and represented by the template. The user may find it advantageous to design or synthesize polynucleotide or polypeptide sequences on the basis of their functional association.
Therefore, the system and methods of the present invention can thus be used in preparing a polynucleotide construct, comprising: identifying a sequence template as statistically associated with an attributes set of interest by a user or client; and preparing a polynucleotide construct having at least one portion operably linked to a context sequence; wherein said context sequence is characterized as having either 80%-85%, 85%-90%, or 90%-100% homology with said sequence template. The user may wish to synthesize said context sequence, by utilizing any synthesis method known in the art for that purpose. Alternatively, the user may construct an expression vector comprising said context sequence or prepare a probe comprising the identified context sequence.
Homology in the range of X %-Y % shall be defined as identity score in the percentage range of X %-Y %. Said identity score is typically provided by an alignment analysis program. The alignment analysis can be performed using a numerous commercial sequence analysis packages, such as, but not limited to WATER (Smith-Waterman local alignment) provided by EMBOSS (European Molecular Biology Open Software Suite) operated with either default values or open gap penalty: 11, extended gap penalty: 0.5, and the default EDNAFULL or BLOSUM62 similarity matrix. Therefore, Homology in the range of %80-%100, as an example, shall mean that an identity score which ranges between 80%400% using WATER according to the parameters set above.
Without limiting the applications of the presently described, the system described above is further adapted to execute the methods described hereinafter. In particular, the method for obtaining a repository of attributes sets, wherein attributes sets are statistically associated with a sequence template representing two or more context sequences, and the method for identifying a sequence template as statistically associated with an attributes set of interest.
Section II
The K-Means algorithm and its derivatives require the initial input of k-criterion from the user. For some clustering purposes, as the present purposes, the initial input of k-criterion is simply not known. For example, the user might not know how many clusters (k) will achieve well separated clusters enriched with functional attributes. It may well be any of 1≧k≧N possibilities; for example where N=16,000 there are 16,000 possibilities.
Furthermore, the results of the K-Means algorithm are extremely sensitive to the initial random selection of cluster representatives. It was recently demonstrated that the worst-case running time of K-Means is super-polynomial i.e. 2Ω(√{square root over (n)})16.
Therefore in one of its embodiments, the present invention utilizes a different computer implemented method (hereinafter: “LBDL (Lower Bound Distance Limit) clustering method”). The LBDL is preferably used for large datasets e.g. N>16000 context sequences, and/or where no prior information relating to the suitable number of clusters is available i.e. k is unknown. While LBDL is preferred over K-means for example, the present invention is not limited to a particular clustering algorithm and may in fact optionally be implemented with any type of clustering.
Accordingly, the LBDL clustering method of the present invention does not require k-criterion at all. Instead, it requires a lower bound distance limit (LBDL) between clusters, as detailed below. This lower bound criterion is advantageous because it encapsulates actual practical meaning to the person skilled in the art i.e. distance between clusters of nucleic or peptide sequences.
The LBDL Clustering Method and Implementation Considerations
For the purposes of the present invention, “lower bound distance limit” shall mean a predetermined real number representing the lower bound distance limit.
For the purposes of the present invention, “lower bound distance limit invariant” shall mean the following invariant (hereafter: the LDBL-invariant): during the execution of the computer implemented LBDL clustering method, clusters will not merge where the distance between them is greater than a given distance limit.
In the present invention “data item”, “heap item”, or “(i,j,d(i,j))” shall mean a data item in a memory structure comprising (i) representing a first template, (j) representing a second template, and d(i,j) the distance between the templates. One of ordinary skill in the art would appreciate that the data item can be presented be other means such as, but not limited to, other data items, or differently ordered data items, all which essentially hold the template information and distance information relating thereto.
The LBDL method is provided hereinafter. In essence, each sequence under analysis is transformed to an information node or, as exemplified below, a sequence template. The algorithm efficiently performs merger operations, until satisfaction of the LBDL criteria. Each unraveled cluster is in turn subjected statistical functional appraisal. Each sequence template representing a cluster of context sequences is stored together with the associated results of the functional appraisal in a repository:












For the purposes of the present application ‘//’ shall mean a comment or remark.










 1.
for each context sequence in dataset allocate a template







// representing the distribution of nucleotides along the sequence.


This step is an initialization step in which each context sequence respectively


represented by a template. A particular embodiment or template representation is


detailed below.










 2.
for each pair (i,j), i ≠ j,i,j ∈ {Context - sequences - in - dataset}










 3.
insert (i,j,d(i,j)) into a multiple-tree-array.







// In steps 2-3 the distance between each pair of templates is measured. Each pair


of templates is then inserted into a multiple-tree-array together with the distance


between them. For clarification (a,b,c) of step 3 represents an abstract data


structure or data item typically comprising 3 numbers, two of which are


identifying a pair of templates and the third is a distance measurement between


them.










 4.
prevMin = −1: List CurMin= Empty List;







// initialization of variables










 5.
While ( ! multiple-tree-array.empty( ) ) {// This is the main loop



 6.
min = multiple-tree-array.DeleteMin( );







// current minimal data item stored in ‘min’. Retrieval of the minimal data item is


typically performed by executing DeleteMin( ) procedure on a multiple-tree-array


data structure. Multiple-tree-arrays are defined below and by definition the


minimal data item is an item having minimum distance held therein i.e. the data


item represents a pair of templates sharing the highest similarity.










 7.
CurMin.Insert(min);







// Insert the minimal data item stored in the multiple-tree-array into CurMin (the


List data structure defined in step 4).










 8.
if (min.distance > lower_bound_distance_limit) Break; }







// The main loop continues until the lower_bound_distance_limit criterion is


satisifed. The Lower Bound Distance limit is defined below. ‘Break’ shall mean


end loop i.e. continue to step 12.










 9.
if (min.distance != prevMin) {







// ‘!=’ means not equal. Therefore, where the condition of step 9 is satisfied, the


previously handled distance stored in ‘prevMin’ is not equal the distance of


current minimum distance i.e. ‘min.distance’. CurMin holds all items which were


retrieved from the multiple-tree-array and are having same distance. This is done


to ensure concurrent and equal treatment of data items which share the same


distance.










10.
HandleCurrentTemplates(CurMin);







// As previously noted, CurMin stores all items which were retrieved from the


multiple-tree-array and are having same distance. HandleCurrentTemplates( ) is a


procedure which is defined below, and in essence this procedure which handles


the merger operation(s) of the currently handled cluster(s).










11.
prevMin = min.distance ; CurMin.Empty( );}







// As all items of CurMin were handled by HandleCurrentTemplates, initialization


of the variables is required to verify that CurMin is empty. ‘Empty( )’ is typically a


procedure which empties the CurMin List. ‘prevMin = min.distance’ updates the


“previous” minimal distance with the current one (in turn the “current” is the


“previous” in the next steps).










12.
Subject each remaining template to a functional appraisal.







// each cluster of context sequences which is represented by a sequence template


are subjected to a functional appraisal. This is typically performed by first


retrieving the names or unique identifiers of genes regulated or affected by the


context sequence within a cluster; and secondly, executing functional appraisal on


the names or unique identifiers retrieved.










13.
Store <Cluster, functional appraisal results> in a repository;}}










In an embodiment, each sequence template(s) or context sequence(s) clusters are stored in a repository together with the associated functional appraisal result. The functional appraisal result can be stored or represented as an attributes set or a list. In an embodiment, the associated functional appraisal is represented by the function attributes array 500. The method therefore obtains a repository of attributes sets, where the attributes set is statistically associated with a sequence template or cluster of context sequences represented thereby.
Typically, a sequence template represents a cluster of two or more context sequences. The later may be either identical context sequences or typically context sequence consisting of different sequences. Moreover, the attributes set associated with a cluster of context sequence(s) can consist of two or more attributes.
A given cluster may also be associated with a particular attribute even where at least one of the context sequence (or gene affected thereby) is not characterized by the attribute. In other words, a cluster may be deemed as statistically associated with an attribute by functional appraisal even where a specific context sequence within the cluster is not particularly characterized by that attribute.
Therefore, a cluster in the present invention may therefore be deemed as a heterogeneous cluster. For the purpose of the present invention “homogeneous cluster” shall mean a context sequence cluster (or sequence template representing said cluster) wherein all context sequences in the cluster are of identical sequence. Alternatively, the term homogeneous cluster shall encompass a context sequence cluster (or sequence template representing said cluster) wherein all genes/context sequences in the cluster are characterized by an attribute. A “heterogeneous cluster” shall mean a sequence context (or sequence template representing said cluster) which is not a homogeneous cluster. In other words, a cluster exhibiting either: (1) at least one pair of non identical context sequences, or (2) statistical association to an attribute wherein at least one gene/context sequence is not characterized by the attribute.
A “heterogeneous repository” shall refer to a repository comprising at least one heterogeneous cluster. Examples 1 to 4 exemplifies numerous heterogeneous clusters detailed in Tables 1 to 4.
In an embodiment, either steps step 12 or 13 further comprise the step of discarding those attributes where the functional appraisal resulted with P_value greater than 0.3, 0.2, 0.1, and preferably greater than 0.05. The person skilled in the art would appreciate that other P_values can be selected for a particular data set in hand.
The lower bound_distance_limit (LBDL) can be set to various values depending on the distance formula used and the sought degree of separation between the clusters. Where the distance formula used is d(V,W) (defined below) and (l) denotes the length of the context sequences, the LBDL can range between 2%×(2 l) to 5%×(2 l), 5%×(2 l) to 20%×(2 l), or 20%×(2 l) to 55%×(2 l). The later is the most preferable as an initial configuration for analysis.
In a one embodiment, the dataset of context sequences is further subjected to multiple sequence alignment. The person skilled in the art would understand multiple sequence alignment can result in gap insertions which in turn may lengthen the length (l) of the context sequences.
By way of an illustration of LBDL invariant, observe the following aligned sequence population (N=2540):
I) 2000 sequences comprising: “AAAAA”
II) 500 sequences comprising: “GGGGG”
III) 30 sequences comprising: “TTTTT”
IV) 5 sequences comprising: “TATAT”
V) 5 sequences: “GTGTG”
With the knowledge that the size of the population is 2540, it is difficult to predict that k=5 (i.e. 5 clusters) will produce well separated clusters of gene sequences (why not try k=6, 7, . . . 1001 and so forth). This is, of course, an exemplary instance. In reality, it may well be that k=1001 will be produce reasonably separated clusters in the vector space.
If the user would enforce k=2 (i.e. two clusters), the K-Means algorithm will cluster the population as follows:
A) 2000 sequences having “AAAAA” as central representative.
B) 540 sequences having effectively “GGGGG” as central representative.
Groups III-V are therefore completely ignored. This might be an unacceptable result. The LBDL clustering method of the present invention avoids this problem. In this regard, ignoring clusters of genes simply because they are relatively small in size is inappropriate and unacceptable because even clusters consisting of even just a few genes may well have great value.
With respect to the above clustering example, assume that the invariant ensures that LBDL=ε>0, ε represent a real number having a positive and almost zero value. For that Lower Bound Distance Limit, the only possible sequence mergers occur among identical sequences i.e. where the distance is 0≦ε. Merging the identical sequences together will result in the original clusters I-V.
In order to perform the clustering of the context sequences, parameterization of each context sequence is required. For that end, at the initialization stage of the clustering method, each context sequence typically requires transformation into a corresponding sequence template.
Distance measurements (d) between any pair of templates V and W can be performed as follows:

    
    
        d←0
        for each i: 0 to l−1
        
            for each aε{A,T,G,C}
            {d+=|V[a,i]−W[a,i]|2}
        
        
    
    


Wherein: (l) denotes the length of the context sequences or alternatively the length or the aligned context sequences.
One of ordinary skill in the art would appreciate that these different distance formulas can be used for the purposes of the present invention. By way of non-limiting example, the distance calculation procedure can be varied such that the fourth step would comprise d+=|V[a,i]−W[a,i]|. Alternatively, the distance calculation procedure can be varied such that the fourth step would comprise d+=|V[a,i]−W[a,i]|t, tεN.
Merger of a pair of context sequence clusters V′ and W′, which are respectively represented by sequence templates V and W, can be defined as follows: The function Merge/Cluster creates and/or returns a sequence template T, representing the cluster T′ consisting of both the context sequences of V′ and W′ (i.e. T′=V′∪W′). The sequence template T would hold the following matrix T4×l as follows:

    
    
        for each i: 0 to l−1
        
            for each aε{A, T, G, C} perform:
        
        
    
    






  {
  
    
      T
      ⁡
      
        [
        
          a
          ,
          p
        
        ]
      
    
    =
    
      
        
          
            
            A
            
          
          ·
          
            V
            ⁡
            
              [
              
                a
                ,
                p
              
              ]
            
          
        
        +
        
          
            
            B
            
          
          ·
          
            W
            ⁡
            
              [
              
                a
                ,
                p
              
              ]
            
          
        
      
      
        
        C
        
      
    
  
  }




This merger procedure can be referred to as “merge”, or “merger”.
In an embodiment, the above merger procedures can handle a merger of more than two context sequence clusters by using sequential merger procedures. By way of non-limiting example, merger of 3 templates may typically require 2 merger operations. As an illustration, the first merger can take place with respect to templates 1 and 2, the product of which can be denoted as new template 12′. A second merger can merge the new template 12′ with template 3 thereby producing a single template 123′ representing all the context sequences which were previously represented by the separate templates 1, 2 and 3.
Memory Allocation of Sequence Templates
Sequence templates as defined above may be designed as a data structure or object. The sequence template essentially represents a subset of context sequences from the dataset i.e. a cluster. The sequence template would, therefore, hold distribution information of each nucleotide at each position in the cluster. The sequence template will typically hold the specific sequences which are grouped together in the cluster represented thereby. Optionally, a sequence template further holds gene name(s) or unique gene IDs which are regulated or otherwise affected by the context sequences within the respective cluster.
At initialization, each sequence in the dataset is transformed to a sequence template.
Order of Merging Operations
For the purposes of the present invention “handling current templates”, “HandleCurrentTemplate( )” and “HandleCurrentTemplates( )” shall have the following meaning. Before the algorithm handles the current templates, any pair of templates (or indeed the clusters represented thereby) having equal distances measured between them are preferably stored in CurMin List. The order of merger the clusters or templates representing them will take place according to the order-invariant as explained and exemplified below.
As described above, the order of merger operations according to the LBDL clustering method is dominated by the distance between the clusters. However, the context sequence dataset might include subsets of numerous clusters having equal or substantially equal distances. The initial order of these clusters or the order of the context sequence may affect to final results of the algorithm. Therefore, in an embodiment, the clustering method of the present invention aims at reducing the sensitivity of the algorithm to the initial order.
To that end, the cluster of context sequences which share equal are handled together without preferring arbitrarily any particular cluster. In particular, where pairs of clusters (or templates representing them) shares a common cluster and the distance between the pair clusters is equal, as illustrated in FIG. 6, they are handled together, as explained below. More formally: given the pair (i,j), and the pair (l,m), (i, j, l, and m are clusters), said pairs will thus be defined as sharing a common cluster if and only if i=l or i=m or j=l or j=m.
The following invariant will therefore apply (henceforth: the order-invariant): As any stage of the execution of a clustering method, the common template having maximum number of neighboring clusters will be the first to merge or be handle i.e. the largest “cluster” of clusters currently (held in CurMin List) will be merged first. Subsequently, the algorithm merges the rest of the currently handled templates according to the order-invariant.
FIG. 6 illustrates, in accordance with one embodiment of the present invention, a simplified example of ascertaining the processing order of templates. (a) and (b), for example, are two clusters of templates having equal distances to a common cluster.
Observe that common template (a) has 4 neighbors and while the central representative of cluster (b) has only 3 neighbors. Therefore, cluster (a) will be processed first. FIG. 7 illustrates the application of the order-invariant according to which cluster (a), previously shown in FIG. 6, was merged prior to handling of cluster (b). As a result, (a′) is a new cluster representing the merger, and (b) is to be handled subsequently according to the order-invariant.
Following the merger operation, the multiple-tree-array is typically updated with all new distances between the pre-existing cluster (or templates representing them) and the newly merged templates.
For each pair of templates (i,j) where the d(i,j)>LBDL, the newly created (i,j,d(i,j)) need not be stored in the multiple-tree-array and can be totally ignored as explained before.
Otherwise, new heap item (i,j,d(i,j)) is inserted into the multiple-tree-array, with a single proviso. Said insertion should takes place unless the distance d(i,j) is lower than min.distance, defined above. In that case, the handling of data items which are held in. CurMin List is temporarily suspended and these data items are re-inserted to the multiple-tree-array.
For example, assume the following data items are held in multiple-tree-array, as follows: (1,5, 120), (5,3, 120), (4,6, 120), (7,4, 125), (1,7, 126), (8,2, 130). Only the first 3 data items will be currently retrieved. These data items share equal distances (120) which is the minimal in the dataset. At a given stage in the execution of the method, these three data items will be held in CurMin List and will be handled together. As the rest of the heap items encapsulate greater distances i.e. 125, 126, and 130, they will be processed later on.
In an embodiment, sorted dictionary data structure is utilized in order to provide fast identification of a common template having the maximal number of neighboring templates. By way of non-limiting example, assume the sorted histogram data structure has the follow data structure: <number of template appearances, sequence template reference>. In the above exemplification, the 3 retrieved data items will generate the following histogram in Sorted dictionary: <2,5>,<1,1>,<1,3>,<1,4>, and <1,6>. The neighbors of template 5 will merge first, under the order-invariant (template referenced as ‘5’; is the common template having maximum number of neighboring clusters).
Complexity Considerations
Utilization of the LDBL-invariant exhibited impressive complexity improvements:
(1) As LBDL based clustering method, by definition, does not require to merge clusters i, and j where the d(i,j)>LBDL, then (i,j,d(i,j)) need not be stored at all i.e. because the cluster pair i and j will never be merged or clustered together. Reduction of memory usage is therefore apparent.
(2) At any stage of the execution, if DeleteMin( ) procedure retrieves the global minimum which is greater (>) than the LBDL, it directly entails that the rest of the data items in the multiple-tree-array also exceed the LBDL. Therefore, the algorithm can be immediately terminated.
In another embodiment, the present invention utilizes a computer implemented method (hereinafter: “Vector Space clustering method”). Alternatively, the VS clustering method is used for performing clustering which is a variant of LBDL method shown above. This VS method is particularly useful where the length of the context sequences is in the range of 3-17 characters. The skilled person in the art would recognize that range is largely affected by computation time, which is associated with the length, and the computer system employed. Computer systems having high computation capabilities may process context sequences of greater length, including but not limited to the range of 10-15, or even 10-20 characters.
The VS clustering method:













1.
for each c = (a1a2a3...a1),ai ∈ {A,T,G,C},1 ≧ i ≧ l {



// for each possible sequence in the vector space of length (l).


2.
List Cluster = null;


3.
for each i ∈ {Context - sequence - in - dataset} {








4.
 double distance = d(c,i);









// calculate the distance between c and i








5.
 if (distance <= lower_bound_distance_limit) {









// cluster together context sequences, if the distance between









them fall within the lower_bound_distance_limit








6.
Cluster.Insert(i);}








7.
Subject Cluster to a functional appraisal;







// each cluster of context sequences which is represented by a sequence


template are subjected to a functional appraisal. This is typically


performed by first retrieving the names or unique identifiers of genes


regulated or affected by the context sequence within a cluster; and


secondly, executing functional appraisal on the names or unique identifiers


retrieved.








8.
Store <Cluster, significant functional appraisal results>







in repository;}}









In a one embodiment, step 1 is replaced with: “for a given sub set of each c=(a1a2a3 . . . al),aiε{A, T, G, C>}, 1≧i≧l;”. In this manner, the method is utilized for a particular subset of context sequences of interest. The latter embodiment can be used to loop through a subset of possible sequences instead of looping through the entire vector space of possible sequences. This may be advantageous for achieving more efficient execution time in cases, for example, that some sequences are known not to feature substantial sequence patterns or important functional characteristics.
The VS differs from the LBDL in several aspects. For example, each context sequence in LBDL is classified into a single cluster. On the other hand, VS may classify each context sequence is several clusters. In that respect CVS is a “softer” classifier which sometimes can be advantageous because a single context sequence may be associated with multiplicity of functional attributes or attributes set. Another difference lies in the fact that VS typically spans thorough the entire vector space of all possible sequences i.e. even sequences which are absent from the context sequences of the data set. This is especially advantageous where synthetic or predicted sequences cannot be found in vivo. This is exemplified in the Step 1, where the analysis is performed for each (c) representing a possible sequence (not necessarily a context sequence of the data set).
Section III
The present invention, in some embodiments, relates to an implementation of specialized memory structures and processes for computations. These structures and processes may optionally be implemented with the embodiments described above and/or may also optionally be used independently.
Memory Module for Holding Parameterized Information
Traditionally, the easiest and most straight forward approach to manage distance information of a dataset is a “distance matrix”. The later typically comprises 2D matrix of distances, such that each cell in said matrix holds the distance between a pair points of a set. A distance matrix is typically a symmetric N×N matrix containing real numbers as elements, given N points in a set. However, in large data sets, as might occur in the present case, the distance matrix performance is unacceptable. The performance time of retrieving the minimal or maximal element stored in the distance matrix is impractical for large data sets i.e. time for retrieving minimal/maximal element stored in the distance matrix.
Consider an exemplary size of the context sequences data set having N=16,000 i.e 16,000 context sequences. The matrix size would supposedly be O(N2) because the distance information represents all pair of said context sequences data set. Utilizing distance matrix would entail a typical retrieval time of a single minimal (or maximal) element in time complexity of O(N2). This renders the 2D distance matrix as unfavorable for use in the present invention, especially in case of large datasets.
In the present invention, “key” is a parameter within a data field comprising a value stored within a data item, or node. Preferably, key is a parameter capable of at least semi-order. By way of non-limiting example, a key may comprise a real number stored in a data item. Where (A) is data item, “KEY(A)” shall mean the parameter within a data field of data item (A). As an example, the key in a data item (i,j,d(i,j)) of the present invention can be the field consisting the distance between the pair of clusters i and j.
“heap” is a data structure based of tree topology that satisfies a general heap invariant as follows: For each pair of elements, items or child nodes in a heap, X and Y: where X is a child node of Y, then KEY(Y)≧KEY(X) i.e. The node having the maximum value as key (“greatest element”) is the top node (or root node) of the heap. This heap is typically referred to a max-heap. Where KEY(Y)≧KEY(X), the smallest element is always the top node, and the heap is referred to as a min heap. “DeleteMin( )” or “deletion” shall mean removing and retrieving the root node of a min-heap. “Insert( )” or “insertion” shall mean adding a new element to a min heap. Heap shall further mean as defined in Corman et al17 which is incorporated herein by reference.
A min heap provides an efficient data structure in which retrieving a minimal element is performed at O(log N). The latter is clearly more efficient in comparison to the traditional distance matrix at about 2 orders in magnitude.
For large data sets, however, a min heap is utterly inappropriate. To hold the complete distance dataset in a min heap is impractical. A PC having 1 GB available RAM and equipped with 3 GHz Intel Pentium processor can handle a min heap of about 300,000 data elements which means that data set cannot be greater than about N=600.
Therefore, in one of its aspects, the present invention provides a “multiple-tree-array” as defined and exemplified below. For the purpose of the present invention, “multiple-tree-array” shall mean memory module or data structure comprised therein employing plurality of tree topologies representing plurality of min-heaps, wherein the plurality of tree topology is managed through a common interface. There the present invention is directed to a computer memory system comprising a plurality of tree topologies representing plurality of (k) heaps, wherein the plurality of tree topologies is managed through a common interface; such that (k≧1).
FIG. 8 illustrates, in accordance with one embodiment of the present invention, a multiple-tree-array topology within a memory module. The top item, the item having the minimum distance, is the element having the minimal key value amongst the (k) min heaps as shown. Therefore, in one embodiment the computer memory system comprises min heaps.
The global minimum in the multiple-tree-array is defined as the minimal element (or minimal root element) amongst the min heaps comprising the multiple-tree-array. In other words, the minimal element is holding the minimal key value in comparison to all (k) min heaps which comprises the multiple-tree-array (hereafter: min-heap invariant). In one embodiment, the global minimum is the minimal distance between a pair of context sequences or sequence templates.
FIG. 8a illustrates similarly, in accordance with another embodiment of the present invention, a multiple-tree-array topology within a memory module. The root element, in this embodiment, is the element having the maximal key value amongst the (k) max heaps as shown. One of ordinary skill in the art would appreciate that while the multiple-tree-array is exemplified herein as a multiple-tree-array comprising min heaps and having a global minimal element, the present invention similarly relates to multiple-tree-array comprising max heaps and having a global maximal element.
In another embodiment, therefore the computer memory system comprises max heaps.
For the purposes of the present invention, “secondary storage” shall mean any data storage system performing slower than typical. RAM (Random Access Memory). Secondary Storage typically includes the non-volatile or semi-permanent storage in a computer environment. Common secondary storage devices are diskettes, hard drives, or tapes.
In an embodiment, each specific heap comprising the multiple-tree-array can be configured to operate as a conventional heap, either min- or max-heap. Insertion of a data item into the multiple-tree-array can be performed by invoking an Insert( ) procedure upon a specific min heap in the multiple-tree-array with one proviso. If the size of the specific min heap reaches a certain predetermined size threshold, another min heap which is selected for the insertion procedure. In the case where all min heaps reached the predetermined size threshold, additional memory comprising min-heap or max-heap is allocated to the multiple-tree-array memory module.
In one embodiment, said size threshold is in the range of 100-1000 elements, 1000-50000 elements, 50000-100000 elements, or 100000-350000 elements. In one embodiment, the element is a data item as defined above.
Deletion of a data item from the multiple-tree-array which comprises min-heaps can be performed by deleting the global minimum of the multiple-tree-array. As defined, global minimum is the minimal top element which holds the minimal key value in comparison to all (k) min heaps comprising in the multiple-tree-array. Following the deletion of the global minimum, the deleted element is replaced by an element from a specific min heap ensuring the heap invariant. That is ensuring that global minimum is the element which holds the minimal key value in comparison to all (k) min heaps comprising in the multiple-tree-array. Where the last element in a min heap is removed the min heap can be released from the multiple-tree-array memory module. Where all the min heaps in the multiple-tree-array memory module have removed their respective last top element, the entire multiple-tree-array memory module is deemed to be empty or null.
The multiple-tree-array provides storage and retrieval performed at the worst case time of O(k log n), where (k) in the number of heaps managed therein.
An “active min heap” and “active subset of min heaps” shall mean the min heaps which are stored in RAM, and at least one of the min heaps stores the global minimum of the multiple-tree-array. A “passive min heap” and “passive subset of min heaps” shall mean the min heaps which are held in secondary storage.
An “active max heap” and “active subset of max heaps” shall mean the max heaps which are stored in RAM, and at least one of the heaps holds the global maximum of the multiple-tree-array. A “passive max heap” and “passive subset of heaps” shall mean the max heaps which are held in secondary storage.
In another embodiment, an active subset of heaps is held in RAM, while the rest of the heaps are maintained on a secondary storage. In another embodiment, a subset of passive min heaps is maintained on secondary storage. In another embodiment, an active subset of max heaps is held in RAM, while the rest of the heaps are maintained on a secondary storage. In another embodiment, a subset of passive max heaps is maintained on secondary storage.
Special attention should be made for ensuring the dominance of the min heap invariant. Where DeleteMin( ) procedure retrieved and erased the global minimum from the multiple-tree-array, the next global minimum may be located at a passive min heap on secondary storage. Therefore, the min heap invariant cannot be ensured with a current active subset of min heaps. The multiple-tree-array is configured to replace or switch at least one of the active min-heap with at least one passive min heap (one of which is storing the current global minimum).
In one embodiment, a data item in a min heap array shall have at least the following members (i,j,d(i,j)) whereby i and j are pointers to respective templates (of the template matrixes) and the third member is a real number representing the distance between the templates i.e. the 3rd field in the data item is the key, the common field as defined above.
In another embodiment, a template (or a context sequence represented thereby) can be erased or invalidated from the data set during the “life time” of the multiple-tree-array. The invalidation may occur upon merger of templates, as described in the present invention. The merger procedure typically entails invalidation of the merged templates. In such a case, at least one existing data item in the multiple-tree-array (i,j,d(i,j)) may be holding distance information relating to the invalidated template. Therefore, said existing data item requires in turn its invalidation or deletion. Typically, such invalidation would require O(2N) deletions of data items from the multiple-tree-array (N be the number of the cluster).
Therefore, in yet another aspect, the present invention is directed to a postponed deletion procedure or postponed invalidation procedure. The deletion is postponed until the operation of DeleteMin( ). The postponed deletion or invalidation of the data item is delayed until their respective deletion by the operation of DeleteMin( ). In other word, instead of searching for the data item for deletion, the multiple-tree-array “awaits” until the invalidated data item is retrieved, by operation of DeleteMin( ). Following the operation of DeleteMin( ), the retrieved data item (i,j,d(i,j)) is verified to be comprising valid data or valid templates (i) and (j).
By way of non-limiting example, validation procedure utilizes a one dimensional array of Boolean values (B) such that B[i] holds #true if and only if template (i) is of valid status. Alternatively, the validation procedure can utilize an array of other validation information such as but not limited to: a time stamp or a string representing a status.
Section IV
The computer implemented method of the present invention for identifying a sequence template as statistically associated with an attributes set of interest typically comprises: (a) providing a repository of attributes sets, said attributes set is statistically associated with a sequence template; (b) selecting an attributes set of interest; and (c) retrieving at least one sequence template statistically associated with said, attributes set. Typically, a sequence template represents two or more context sequences. Moreover, the attributes set can consist of two or more attributes of interest selected by a user or client. The retrieved sequence template of step (c) typically also represents two or more context sequences. Optionally, retrieved sequence template or cluster represented thereby is a heterogeneous cluster.
In an embodiment, the repository was obtained according to any method of the present invention. In particular, the repository can be obtained by utilization of the LBDL clustering method. In another embodiment, the repository was obtained by utilization of the VS clustering method. Optionally, the repository is a heterogeneous repository.
Attributes or function attributes of interest can be selected for from the group consisting: the Gene Ontology Project (GO), Interpro annotation (European Molecular Biology Laboratory, EMBL), SMART (a Simple Modular Architecture Research Tool, found at (smart.embl-heidelberg.de), UniProt Knowledgebase (SwissProt), OMIM (by NCBI) PROSITE (by the Swiss Institute of Bioinformatics), Protein Information Resource (PIR), GeneCards, and Kyoto Encyclopedia of Genes and Genomes (KEGG).
For the purposes of the present invention, “similarity”, “similarity degree”, or “sd” between any pair of function attributes arrays V, and W can be determined by the following procedure:















sd ← 0



For each a ∈ {complete - function - attributes - set} {



// for each attribute in the complete function attributes array,



sum up the differences or divergence between the respective



real values



if (V[a].value == #true and W[a].value == #false) {sd++;}



// as different increase the distance by 1



if (V[a].value==false and W[a].value==true) {sd++;}



}










Wherein:
(a)—represents a particular function attribute name; and
V[a]·value—represents a value associated to particular function (a).
V and W comprises binary digits as values;
Where V and W comprises real numbers as values, “similarity” between any pair of function attributes arrays V, and W can be determined by the following procedure:















sd ← 0



For each a ∈ {complete - function - attributes - set}{



// for each attributes in the function attribute array, sum up



the differences or divergence between the respective real



values



sd+=| V[a].value − W[a].value |



}










Wherein:
(a)—represents a particular function attribute name; and
V[a]·value—represents a value associated to particular function (a).
One of ordinary skill in the art would understand that either V and/or W may not comprise a particular function attribute. This scenario can be represented as: V[a]·value=null i.e. particular function attribute ‘a’ is not associated with V. In such a case, the value may be deemed to have a default value or another symbol which represent a null value.
In an embodiment, where the attributes array features an array of real numbers as values, ‘0.0’ may be deemed to represents a non inclusion of a particular function.
In an embodiment, the above step of (sd+=|V[a]·value−W[a]·value|) can be performed if and only if (V[a]·value !=null and W[a]·value !=null). Thus, null valued attributes are ignored.
One of ordinary skill in the art would understand that similarity degree can be determined by the above distance measurement between a pair of function attribute arrays. However, many alternative approaches may be adopted to provide a measure of similarity between function attribute arrays.
For the purposes of the present invention, “functional significance appraisal”, “functional appraisal”, “attribute appraisal” and “functional significance test” shall mean refer to a computational method comprising a statistical test yielding confidence-level or probability, P_value that at least one function attribute is associated with a given gene cluster or gene cluster regulated or otherwise affected by context sequence(s).
The typical input for this computational method is the names or unique identifiers of genes regulated or otherwise affected by the context sequence within a cluster.
The typical result (or output) of functional appraisal is typically a list of attributes which can be deemed as statistically over represented within said input cluster. The list of attributes can further comprise the P_value or confidence level of an attribute within the list.
By way of another non-limiting example, the statistical test can be based on Fisher exact probability test, or hyper-geometric (HG) probability distribution pertaining the sampling without replacement from finite population as explained hereinafter. By way of illustration, N typically denotes the entire size of the gene population (i.e. population size); n denotes the size of context sequence cluster under analysis (i.e. sample size); m denotes the number of genes in the entire population characterized by at least one function attribute (i.e. the “unique” group size); k denotes the number of unique items found in the cluster under analysis. For example, assume N=16,231, n=197, m=678, and k=20 the P_value is therefore 0.0001467. The hypergeometric distribution with parameters N, m and n, and k, can therefore define the probability of getting exactly k genes characterized by said function attribute in a cluster of input genes (or context sequence cluster regulating or affecting them).
Jackknife methodologies and other confidence assisting procedures can be added to increase the confidence level of the enrichment results. Functional appraisal tools can be purchased in, for example, (david.abcc.ncifcrf.gov)18,19.
In one embodiment, the retrieval of a sequence template statistically associated with an attributes set of interest comprises: determining similarity between the attributes set of interest and each attributes set previously inserted into repository; and retrieving from the repository a sequence template associated with at least one attributes set previously inserted into said repository.
The repository can typically comprise (N) pair(s) of sequence templates and their associated attributes set: <Ti,ASi>, 1≧i≧N, where Ti, and ASi are a sequence template and attributes set of the i-th record in the repository, respectively. The method of retrieval of a sequence template statistically associated with an attributes set (AS) of interest, can therefore be performed by: (a) determining similarity, by utilizing similarity formula such as, but not limited to ds(AS,ASi), as defined above; and (b) retrieval of <Ti,ASi>, 1≧i≧N from the repository together with the respective, ds(AS,ASi).
The order of retrieved records is preferably in descending order according to the similarity degree. The retrieved sequence template typically also represents two or more context sequences. The later may be either identical context sequences or typically context sequence consisting of different sequences.
Moreover, the attributes set associated with the context sequence(s) or sequence template can consist of two or more attributes. Optionally, the context sequence(s) or sequence template may be statistically associated with a particular attribute even where at least one of the context sequence (or gene affected thereby) is not characterized by the attribute. In other words, the retrieval procedures of the present invention therefore enable retrieval of heterogeneous clusters, as defined above.
The retrieval of a sequence template statistically associated with said attributes set, may comprises the steps of: determining similarity between the attributes set of interest and at least one attributes set previously inserted into repository; and retrieving from the repository a sequence template associated with the at least one attributes set previously inserted into said repository.
The repository can therefore typically comprise (N) of pair(s) of sequence templates and their associated attributes set: <Ti,ASi>, 1≧i≧N, where Ti, and ASi are a sequence template and attributes set of the i-th record in the repository, respectively. The method of retrieval of a sequence template statistically associated with an attributes set (AS) of interest, can therefore be performed by: (a) determining similarity, by utilizing similarity formula such as, but not limited to ds(AS,ASi), as defined above; and (b) retrieval at least one of <Ti,ASi>, 1≧i≧N from the repository together with respective ds(AS,ASi). The order of retrieved records is preferably in descending order according to the similarity degree.
The retrieved sequence template typically also represents two or more context sequences. The later may be either identical context sequences or typically context sequence consisting of different sequences.
In the above embodiments, the method typically retrieves at least one sequence template together with a degree of similarity between the attributes set of interest and the attributes set statistically associated with the sequence template. However, filtering of at least one sequence template is typically required.
To that end, in another optional embodiment, the retrieving includes discarding a sequence template associated with said at least one attributes set, where the similarity between said at least one attributes set and the attributes set is above a predefined threshold (L). In that respect therefore, the retrieval further comprises discarding (or filtering out) records having ds(AS, ASi)≧(L).
The threshold (L) can be set to various values depending on the number of results sought by the user or the client. As an alternative, the user or client may wish to retrieve the best result alone.
To that end, the retrieving step includes discarding a sequence template associated with said at least one attributes set, where the similarity between said at least one attributes set and the attributes set of interest is above the global minimum. In that respect therefore, the retrieval further comprises discarding (or filtering out) records having ds(AS,ASi)>min1≧j≧N(ds(AS,ASj)).
In an embodiment, said retrieving includes discarding attributes (i.e. members of the attributes set) where the functional appraisal resulted with a respective P_value greater than 0.3, 0.2, 0.1, or preferably greater than 0.05. The person skilled in the art would appreciate that other P_values ranges can be selected for a particular data set in hand.
Following retrieval of the two or more sequence template statistically associated with said attributes set of interest, the method can further comprise merging at least two of retrieved sequence template (or clusters represented thereby). Merger procedure is detailed above.
Section V—Experimental Examples
This Section relates to experimental examples, illustrating the above embodiments of the present invention. These examples are provided for the purpose of illustration only and without any intention of being limiting in any way.
Example 1: Arabidopsis Thaliana 
A. Dataset
The complete RefSeq sequences of plants mRNA was downloaded (www.ncbi.nlm.nih.gov/RefSeq). The database was filtered in order to exclusively include mRNA sequences of Arabidopsis Thaliana. The dataset was thereafter cleaned of duplicate genes to reduce over representation of identical genes. The translation initiator codon was identified using the Reveq CDS. Sequence in the length of 9 nucleotides preceding translation initiator codon were parsed, and indexed. The dataset thereafter included the total of 16,491 short sequences of 9 successive nucleotides. The complete dataset was aligned.
B. Application of the LBDL Clustering Method
The LBDL clustering method was applied on the mRNA dataset in 8 separate phases. In each phase the algorithm was provided with a different Lower Bound Distance Limit so as to cluster with varying degree of stringency (0.01; 2.01; 3.01; 4.01; 5.01; 6.01; and 7.01). The separate phase analysis provides an opportunity to investigate smaller more exotic clusters of genes before they merge into larger cluster and lose some significant functional properties along the way.
C. Significant Functional Enrichments of Plant Gene Clusters
Table 1 prescribes the emerging gene clusters which were identified by LBDL clustering method. This table includes selected clusters which demonstrated significant functional attributes.
The clusters in Table 1 are arranged according to size i.e. number of different genes in each cluster. For each cluster, said table provides a template comprising matrix T4×9, where the distribution of nucleotides for each position preceding the translation initiation codon. For convenience, the most frequent sequence of successive nucleotides, is disclosed i.e. the dominant context sequence.
The translation initiation codon is at position ‘0’ and does not appear in the table. Table 1 includes a portion of results due the amount of information the LBDL clustering method extracted and collected.
For each template disclosed, the table provides the significant functions or functional attributes set associated with the template. The largest gene cluster includes some 1613 distinct genes. The second largest cluster has 1433 distinct genes. These clusters seem to support previous work which stipulated the A-rich conserved region in higher plants20. The large clusters were enriched, inter alia, with genes encoding nuclear and transcription related proteins, partially in contradiction to previous speculations21. Another observation is that the smaller clusters tend to be quite distant from the largest gene clusters. Smaller clusters tend also to include non-A nucleotides with distribution above 80%. For easier reference these nucleotides were highlighted in the body of the table.
As now shown in Table 1, the dominant context sequence ‘tttttaaaa’ is clearly associated for the first time with response to abiotic stimulus and further chemical stimulus. Moreover, a plurality of dominant context sequences are now associated with transcription regulation and transcription in general. For example, templates associated with transcription regulation consists, inter alia, of: ‘aaaaaaaaa’, ‘gttaagaaa’, ‘ttttcttca’ and ‘gagagagaa’. Photosynthesis is associated with ‘acaaaaaca’, and also ‘gaagaagaa’. This unravels the fact that as many as a single function can be associated to a plurality of context sequences or dominant context sequences with strong statistical significance. Table 1 illustrates plurality of other templates and their association with significant functional attributes.
The statistically supported association of functional attribute arrays with a template can be used both in research and genetic engineering.
Example 2: Homo sapiens 
A. Dataset
The complete RefSeq sequences of Human mRNA were downloaded (www.ncbi.nlm.nih.gov/RefSeq). The database was filtered in order to exclusively include mRNA sequences of Homo sapiens. The dataset was thereafter cleaned of duplicate genes to reduce over representation of identical genes. The translation-initiator codon was identified using the RefSeq CDS. Sequence in the length of 9 nucleotides preceding translation initiator codon were parsed, and indexed. The dataset thereafter included the total of 17,053 short sequences of 9 successive nucleotides. The complete dataset was aligned.
B. Application of the LBDL Clustering Method
The LBDL clustering method was applied on the mRNA dataset in 3 separate phases. In each phase the algorithm was provided with a different Lower Bound Distance Limit so as to cluster with varying degree of stringency (5.01; 6.01; and 7.01). The separate phase analysis provides an opportunity to investigate smaller more exotic clusters of genes before they merge into larger cluster and lose some significant functional properties along the way.
C. Significant Functional Enrichments of Human Gene Clusters
Table 2 prescribes the emerging gene clusters which were identified by LBDL clustering method. This table includes selected clusters which demonstrated significant functional attributes.
The clusters in Table 2 are arranged according to size i.e. number of different genes in each cluster. For each cluster, said table provides a template comprising matrix T4×9 where the distribution of nucleotides for each position preceding the translation initiation codon. For convenience, the most frequent sequence of successive nucleotides, is disclosed i.e. the dominant context sequence.
The translation initiation codon is at position ‘0’ and does not appear in the table. Table 2 includes only a portion of the results due the amount of information the LBDL clustering method extracted and collected.
The most significant functional enrichment of each cluster appears as well. The largest gene cluster includes some 1562 distinct genes. The second largest cluster has 987 distinct genes.
Another observation is that the smaller clusters tend to be quite distant from the largest gene clusters.
As now shown in Table 2, the context sequence ‘gccagcacc’ can be associated with response to pest, or pathogen. Importantly the same context sequence is statistically associated with immunoglobulin and the immune system. Moreover, plurality of context sequences are now associated with transcription regulation and transcription in general. For example, templates associated with transcription regulation consists, inter alia, of: ‘cgcgggaag, ‘ggaggaaaa’, and ‘ctgaagaaa’. Metabolism is statistically associated with ‘cccgccgcg’, ‘agcctagaa’ and also ‘ctgaagaaa’. Again, as many as a single function can be associated to a plurality of context sequences with strong statistical significance. Table 2 illustrates plurality of other templates and their association with a significant functional attributes.
The statistically supported associating functional attribute arrays with a template can be used both in research and genetic engineering.
Example 3: Mus Musculus 
A. Dataset
The complete RefSeq sequences of Mus Musculus mRNA was downloaded (www.ncbi.nlm.nih.gov/RefSeq). The database was filtered in order to exclusively include mRNA sequences of Mus Musculus. The dataset was thereafter cleaned of duplicate genes to reduce over representation of identical genes. The translation initiator codon was identified using the RefSeq CDS. Sequence in the length of 9 nucleotides preceding translation initiator codon were parsed, and indexed. The dataset thereafter included the total of 15,312 short sequences of 9 successive nucleotides. The complete dataset was aligned.
B. Application of the LBDL Clustering Method
The LBDL clustering method was applied on the mRNA dataset in 3 separate phases. In each phase the algorithm was provided with a different Lower Bound Distance Limit so as to cluster with varying degree of stringency (5.01; 6.01; and 7.01). The separate phase analysis provides an opportunity to investigate smaller more exotic clusters of genes before they merge into larger cluster and lose some significant functional properties along the way.
C. Significant Functional Enrichments of Plant Gene Clusters
Table 3 prescribes the emerging gene clusters which were identified by LBDL clustering method. This table includes selected clusters which demonstrated significant functional attributes.
The clusters in Table 3 are arranged according to size i.e. number of different genes in each cluster. For each cluster, said table provides a template comprising matrix T4×9, where the distribution of nucleotides for each position preceding the translation initiation codon. For convenience, the most frequent sequence of successive nucleotides, is disclosed i.e. the dominant context sequence.
The translation initiation codon is at position ‘0’ and does not appear in the table. Table 3 includes only a portion of the results due the amount of information the LBDL clustering method extracted and collected.
The most significant functional enrichment of each cluster appears as well. The largest gene cluster includes some 1197 distinct genes. The second largest cluster has 710 distinct genes.
As now shown in Table 3, the context sequence ‘gccgccgcc’ can be associated with sh3 domain. Moreover, plurality of context sequences are now associated with metabolism in general. For example, templates associated with metabolism consists, inter alia, of: ‘ccccgcgcc, and ‘cggaggaag’. Metal ion binding is statistically associated with both ‘gccgccgcc’, and ‘ccccgcgcc’. Again, as many as a single function can be associated to a plurality of context sequences with strong statistical significance. Table 3 illustrates plurality of other templates and their association with a significant functional attributes.
The statistically supported associating functional attribute arrays with a template can be used both in research and genetic engineering.
Example 4: Bos Tauros 
A. Dataset
The complete RefSeq sequences of Bos Tauros mRNA was downloaded (www.ncbi.nlm.nih.gov/RefSeq). The database was filtered in order to exclusively include mRNA sequences of Bos Tauros. The dataset was thereafter cleaned of duplicate genes to reduce over representation of identical genes. The translation initiator codon was identified using the RefSeq CDS. Sequence in the length of 9 nucleotides preceding translation initiator codon were parsed, and indexed. The dataset thereafter included the total of 9,723 short sequences of 9 successive nucleotides. The complete dataset was aligned.
B. Application of the LBDL Clustering Method
The LBDL clustering method was applied on the mRNA dataset in 3 separate phases. In each phase the algorithm was provided with a different Lower Bound Distance Limit so as to cluster with varying degree of stringency (5.01; 6.01; and 7.01). The separate phase analysis provides an opportunity to investigate smaller more exotic clusters of genes before they merge into larger cluster and lose some significant functional properties along the way.
C. Significant Functional Enrichments of Plant Gene Clusters
Table 4 prescribes the emerging gene clusters which were identified by LBDL clustering method. This table includes selected clusters which demonstrated significant functional attributes.
The clusters in Table 4 are arranged according to size i.e. number of different genes in each cluster. For each cluster, said table depicts the distribution of nucleotides for each position preceding the translation initiation codon. For convenience, the most frequent sequence of successive nucleotides, is disclosed i.e. the dominant context sequence.
The clusters in Table 4 are arranged according to size i.e. number of different genes in each cluster. For each cluster, said table provides a template comprising matrix T4×9, where the distribution of nucleotides for each position preceding the translation initiation codon together with the most frequent sequence of successive nucleotides, is disclosed. Table 4 illustrates plurality of other templates and their association with a significant functional attributes.
The most significant functional enrichment of each cluster appears as well. The largest gene cluster includes some 815 distinct genes. The second largest cluster has 583 distinct genes.
Example 1-4 exemplify numerous heterogeneous clusters detailed in Tables 1-4 which were identified by the method and systems of the present invention.







TABLE 1





Emerging gene clusters which were identified by the clustering algorithm pertaining Arabidopsis Thaliana.


The below clusters are arranged according to declining size. For each cluster, the table


depicts the distribution of nucleotides for each position along the context sequence.

















Size of Cluster

Distribution of nucleotides per position


(number of context
Function attributes set (Enrichment
along the context sequence (%)












sequences)
score/P_value/Benjamini)
Pos:
−9
−8
−7





1613
membrane (9.88, 7.0E−17, 4.1E−14); transmembrane

a
a
a



(9.88, 9.0E−14, 2.2E−11); transit peptide (6.7, 5.5E−12,
A %
46.12
71.60
67.45



6.7E−10); chloroplast (6.7, 4.5E−9, 3.0E−7); plastid (6.7,
T %
10.78
9.051
1.921



1.7E−6, 7.7E−5); signal (6.14, 4.7E−12, 6.9E−10);
G %
33.84
13.63
26.10



glycoprotein (6.14, 3.7E−11, 3.0E−9); response to abiotic
C %
9.237
5.703
4.525



stimulus (3.54, 3.3E−6, 3.3E−3); response to chemical



stimulus (3.54, 1.1E−5, 7.1E−3); response to hormone



stimulus (3.54, 2.2E−3, 4.7E−1); response to endogenous



stimulus (3.54, 4.8E−3, 5.9E−1); metal-binding (3.54,



4.6E−12, 8.5E−10); iron (3.54, 8.0E−12, 8.4E−10);



oxidoreductase (3.54, 1.1E−11, 1.0E−9); heme (3.54,



2.5E−8, 1.5E−6); monooxygenase (3.54, 3.6E−6, 1.5E−4);



E-class P450, group I (3.54, 1.7E−4, 4.9E−1); dna-binding



(2.77, 3.4E−4, 1.0E−2); nuclear protein (2.77, 1.4E−3,



3.5E−2); transcription (2.77, 3.4E−3, 6.8E−2);



transcription regulation (2.77, 5.2E−3, 9.1E−2);



ribonucleoprotein (2.26, 1.2E−9, 8.9E−8); ribosomal



protein (2.26, 6.9E−8, 3.9E−6); structural molecule



activity (2.26, 4.0E−5, 3.3E−2); structural constituent of



ribosome (2.26, 8.9E−4, 3.9E−1); zinc (0.23, 8.8E−2, 5.8E−1);


1433
transit peptide (5.12, 2.7E−9, 5.0E−7); plastid (5.12, 1.9E−6,

t
t
t



1.7E−4); chloroplast (5.12, 9.5E−6, 5.8E−4); metal-
A %
27.70
9.560
11.16



binding (3.84, 2.9E−13, 2.2E−10); zinc (3.84, 8.4E−9,
T %
42.07
50.66
48.98



1.2E−6); zinc-finger (3.84, 3.2E−8, 3.9E−6); response to
G %
12.00
28.68
19.46



abiotic stimulus (3.73, 7.1E−6, 7.2E−3); response to
C %
18.21
11.09
20.37



chemical stimulus (3.73, 6.4E−5, 4.2E−2); response to



stimulus (3.73, 3.8E−4, 1.4E−1); response to endogenous



stimulus (3.73, 7.2E−4, 1.9E−1); response to hormone



stimulus (3.73, 1.9E−3, 3.5E−1); nuclear protein (3.5,



3.4E−11, 8.2E−9); dna-binding (3.5, 5.4E−6, 3.6E−4);



transcription (3.5, 4.2E−4, 1.3E−2); transcription



regulation (3.5, 1.5E−3, 3.6E−2); membrane (3.42, 3.4E−6,



2.5E−4); transmembrane (3.42, 1.7E−5, 9.4E−4); signal



(2.61, 1.6E−7, 1.6E−5); glycoprotein (2.61, 3.6E−5, 1.8E−3);



translation regulator activity (2.43, 1.5E−4, 1.2E−1);



translation factor activity, nucleic acid binding (2.43,



1.5E−4, 1.2E−1); protein biosynthesis (2.43, 2.8E−4, 1.1E−2);



response to external stimulus (2.31, 3.3E−4, 1.5E−1);



defense response to pathogen, incompatible interaction



(2.31, 4.9E−4, 1.5E−1); response to wounding (2.31, 2.5E−3,



3.7E−1); response to abscisic acid stimulus (2.17, 3.3E−3,



4.3E−1); response to water (2.17, 8.6E−3, 6.9E−1);



peroxisome (2.05, 4.1E−4, 1.3E−2); gibberellin signaling



pathway (1.97, 7.5E−4, 2.2E−2); zinc (1.89, 8.4E−9, 1.2E−6);



zinc-finger (1.89, 3.2E−8, 3.9E−6); Nuclear protein



(1.89, 7.5E−2, 5.5E−1); meristem development (1.81,



1.6E−3, 3.3E−1); elongation factor (1.8, 1.6E−3, 3.9E−2);



translation elongation factor activity (1.8, 2.0E−3, 5.7E−1);



developmental protein (1.74, 3.2E−4, 1.2E−2); defense



response to pathogen, incompatible interaction (1.71,



4.9E−4, 1.5E−1); golgi stack (1.69, 5.4E−3, 1.1E−1);



protein transport (1.69, 9.7E−3, 1.8E−1); ribosomal



protein (1.64, 2.7E−5, 1.4E−3);


1345
transit peptide (5.07, 2.5E−10, 9.1E−8); mitochondrion

g
t
t



(5.07, 1.2E−3, 2.9E−2); membrane (4.47, 3.7E−8, 4.6E−6);
A %
15.76
25.27
20.74



transport (4.47, 2.2E−6, 1.4E−4); transmembrane (4.47,
T %
31.37
36.05
49.21



2.5E−5, 1.1E−3); plastid (4.05, 1.9E−3, 4.3E−2); amino-
G %
38.43
13.75
22.52



acid biosynthesis (2.15, 1.0E−5, 5.4E−4); DNA-directed
C %
14.42
24.90
7.509



RNA polymerase activity (2.13, 1.2E−4, 9.3E−2); RNA



POLYMERASE (2.13, 4.6E−4, 5.1E−2); PURINE



METABOLISM (2.13, 1.9E−2, 5.1E−1); dna-directed rna



polymerase (2.13, 2.4E−2, 3.0E−1); PYRIMIDINE



METABOLISM (2.13, 2.6E−2, 5.3E−1);



ribonucleoprotein (2.03, 2.1E−8, 3.9E−6); ribosomal



protein (2.03, 2.8E−8, 4.2E−6); cytosolic ribosome (sensu



Eukaryota) (2.03, 2.4E−4, 5.0E−2); structural constituent



of ribosome (2.03, 3.5E−3, 6.9E−1); cytosol (2.03, 6.2E−3,



3.6E−1); RIBOSOME (2.03, 4.7E−2, 6.0E−1); nuclear



protein (1.84, 5.4E−4, 1.6E−2); transcription (1.84, 1.8E−2,



2.5E−1); dna-binding (1.84, 6.2E−2, 5.2E−1);



transcription regulation (1.84, 7.2E−2, 5.5E−1);



glycoprotein (1.8, 3.1E−5, 1.3E−3); signal (1.8, 5.5E−3,



1.1E−1); gtp-binding (1.73, 1.8E−5, 8.3E−4); P-loop (1.73,



6.9E−5, 2.7E−3); nucleotide binding (1.73, 1.5E−4, 5.6E−3);



GTP binding (1.73, 4.0E−3, 8.3E−2); lipoprotein (1.73,



1.0E−2, 1.6E−1); rna-binding (1.58, 1.8E−4, 6.2E−3);



metal-binding (1.49, 2.3E−9, 5.7E−7); zinc (1.49, 1.1E−6,



9.6E−5); zinc-finger (1.49, 6.4E−6, 3.9E−4);


751
transit peptide (6.85, 6.3E−11, 2.3E−8); plastid (6.85,

a
c
a



2.9E−8, 7.0E−6); chloroplast (6.85, 2.3E−7, 4.3E−5);
A %
60.85
26.76
85.08



transit peptide: Chloroplast (6.85, 9.2E−4, 5.1E−1);
T %
14.38
5.326
3.728



apoplast (3.2, 5.7E−6, 5.9E−4); Germin (3.2, 1.8E−5, 7.0E−2);
G %
9.720
32.09
4.127



Cupin 1 (3.2, 2.1E−5, 4.2E−2); Cupin region (3.2,
C %
15.04
35.81
7.057



3.0E−5, 3.9E−2); signal (3.2, 1.4E−4, 1.3E−2);



glycoprotein (3.2, 1.6E−4, 1.3E−2); cell wall (3.2, 5.7E−4,



3.2E−2); manganese (3.2, 6.2E−4, 3.2E−2); metal ion-



binding site: Manganese (3.2, 2.2E−3, 5.7E−1); response to



stimulus (2.96, 2.5E−5, 5.0E−2); response to abiotic



stimulus (2.96, 3.5E−5, 3.5E−2); response to chemical



stimulus (2.96, 2.9E−3, 6.2E−1); transmembrane (2.11,



4.4E−4, 2.9E−2); membrane (2.11, 1.2E−3, 4.7E−2); EFh



(2, 2.1E−3.5, 2E−1);


680
signal (3.44, 8.0E−6, 5.9E−3); multigene family (3.44,

a
a
t



1.4E−5, 5.0E−3); glycoprotein (3 .44, 7.3E−5, 1.3E−2);
A %
46.76
40.44
17.64



oxidoreductase (2.6, 3.3E−5, 8.1E−3); iron (2.6, 7.6E−3,
T %
25.44
35.73
35.58



2.7E−1); membrane (2.55, 1.8E−4, 2.2E−2);
G %
10.14
10.44
28.38



transmembrane (2.55, 6.6E−4, 4.7E−2); transit peptide
C %
17.64
13.38
18.38



(2.21, 7.8E−4, 5.1E−2); plastid (2.21, 1.2E−3, 6.2E−2);



chloroplast (2.21, 1.4E−2, 4.2E−1); systemic acquired



resistance (2.04, 8.3E−5, 1.6E−1);


680
transit peptide (3.84, 3.5E−7, 1.3E−4); plastid (3.84, 2.4E−4,

a
a
a



2.1E−2); chloroplast (3.84, 3.5E−4, 2.8E−2); nuclear
A %
34.41
48.97
68.08



protein (3.65, 5.6E−5, 8.2E−3); transcription regulation
T %
32.64
11.17
10.44



(3.65, 1.7E−4, 2.1E−2); transcription (3.65, 3.6E−4, 2.6E−2);
G %
17.20
23.38
10.58



dna-binding (3.65, 6.8E−4, 4.4E−2); chloroplast (3.65,
C %
15.73
16.47
10.88



5.0E−5, 2.1E−2); plastid (3.65, 7.5E−5, 1.6E−2); calcium



(1.69, 1.2E−3, 6.3E−2); EF hand (1.69, 1.6E−2, 4.2E−1);



DNA-binding (1.42, 1.8E−4, 1.9E−2)


655
plastid (, 1.1E−11, 4.8E−9); chloroplast (, 1.2E−11, 2.6E−9);

t
t
t



nuclear protein (3.09, 2.1E−4, 1.5E−2); transcription
A %
19.38
7.022
11.45



regulation (3.09, 4.0E−4, 2.7E−2); transcription (3.09,
T %
39.23
62.29
43.66



8.4E−4, 5.0E−2); dna-binding (3.09, 6.0E−3, 2.5E−1);
G %
21.22
7.175
4.274



transit peptide (1.96, 1.1E−4, 9.8E−3); plastid (1.96, 1.3E−2,
C %
20.15
23.51
40.61



4.5E.1); kinase (1.65, 9.6E−8, 7.0E−5); transferase



(1.65, 4.3E−7, 1.6E−4); nucleotide-binding (1.65, 4.5E−6,



1.1E−3); serine/threonine-protein kinase (1.65, 1.1E−5,



1.6E−3); atp-binding (1.65, 2.0E−5, 2.5E−3); auxin



signaling pathway (1.46, 1.9E−2, 5.3E−1); zinc-finger



(1.09, 7.3E−6, 1.3E−3); zinc (1.09, 8.1E−5, 8.5E−3); metal-



binding (1.09, 2.1E−3, 1.1E−1); calcium (0.92, 1.4E−2,



4.5E−1);


618
response to hormone stimulus (3.85, 1.2E−5, 2.5E−2);

a
a
t



response to chemical stimulus (3.85, 1.5E−5, 1.5E−2);
A %
35.76
53.55
17.63



response to abiotic stimulus (3.85, 2.4E−5, 1.6E−2);
T %
29.12
21.03
63.26



response to endogenous stimulus (3.85, 2.9E−4, 1.4E−1);
G %
21.19
2.427
6.634



response to auxin stimulus (3.85, 1.9E−3, 4.8E−1);
C %
13.91
22.97
12.45



response to stimulus (3.85, 3.0E−3, 5.8E−1); membrane



(3.55, 1.6E−7, 5.9E−5); metalloprotein (0.89, 3.3E−2,



5.7E−1); chromoprotein (0.89, 3.9E−2, 6.0E−1); nuclear



protein (0.87, 4.0E−2, 6.0E−1); Membrane (0.62, 5.1E−2,



6.4E−1); rna-binding (0.4, 4.2E−2, 5.9E−1); nucleotide-



binding (0.12, 1.7E−2, 4.1E−1);


462
nuclear protein (3.2, 2.1E−7, 1.5E−4); transcription (3.2,

g
a
g



3.3E−5, 1.2E−2); transcription regulation (3.2, 4.8E−5,
A %
11.47
76.19
15.36



1.2E−2); Transcription factor, K-box (3.2, 2.0E−4, 5.5E−1);
T %
8.225
3.030
7.792



domain: K-box (3.2, 2.4E−4, 8.8E−2); domain: MADS-
G %
74.89
15.15
74.89



box (3.2, 2.4E−4, 8.8E−2); coiled coil (3.2, 4.0E−4, 4.1E−2);
C %
5.411
5.627
1.948



activator (3.2, 6.8E−4, 5.4E−2); dna-binding (3.2,



9.7E−4, 6.9E−2); flowering (3.2, 1.8E−2, 5.9E−1);



developmental protein (3.2, 2.2E−2, 6.1E−1);



differentiation (3.2, 2.8E−2, 6.8E−1); transport (1.9, 5.7E−5,



8.4E−3); membrane (1.9, 1.6E−2, 5.7E−1); zinc (0.48,



1.4E−2, 5.5E−1); ion transport (0.42, 2.1E−2, 6.3E−1);



transferase (0.38, 2.6E−4, 3.1E−2);


457
response to abiotic stimulus (2.11, 1.1E−3, 6.9E−1);

g
a
a



response to chemical stimulus (2.11, 1.7E−3, 6.7E−1);
A %
10.50
82.93
96.93



transit peptide (2.02, 1.0E−4, 1.9E−2); chloroplast (2.02,
T %
5.032
1.969
0.656



1.1E−2, 3.4E−1); plastid (2.02, 1.2E−2, 3.5E−1);
G %
67.83
5.908
1.312



photosynthesis (2.02, 1.4E−2, 3.7E−1); thylakoid (2.02,
C %
16.63
9.190
1.094



1.8E−2, 4.1E−1); zymogen (1.95, 9.0E−6, 6.6E−3);



propeptide: Activation peptide (1.95, 8.1E−4, 4.6E−1);



thiol protease (1.95, 2.4E−3, 1.2E−1); protease (1.95,



2.6E−3, 1.2E−1); signal (1.95, 6.0E−3, 2.2E−1); nuclear



protein (1.87, 3.8E−4, 3.9E−2); activator (1.87, 1.1E−3,



6.6E−2); dna-binding (1.87, 1.6E−2, 3.9E−1); transcription



(1.87, 2.9E−2, 5.5E−1); transcription regulation (1.87,



3.5E−2, 6.0E−1); oxidoreductase (1.49, 2.1E−5, 5.1E−3);



monooxygenase (1.49, 1.9E−4, 2.8E−2); iron (1.49, 8.7E−4,



5.7E−2); Membrane (1.49, 4.2E−3, 1.8E−1);


375
nuclear protein (1.48, 3.9E−4, 9.1E−2); response to light

a
a
a



stimulus (1.44, 3.2E−4, 4.8E−1); response to radiation
A %
48.26
29.86
55.46



(1.44, 3.5E−4, 3.0E−1); flavoprotein (1.33, 1.9E−2, 5.8E−1);
T %
16
22.66
3.733



oxidoreductase (1.19, 4.0E−3, 3.1E−1); iron (1.19,
G %
19.73
21.06
5.333



1.8E−2, 6.1E−1); transit peptide (1.07, 6.9E−3, 4.0E−1);
C %
16
26.4
35.46



signal (1.06, 1.4E−3, 1.9E−1); iron (0.89, 1.8E−2, 6.1E−1);



metal-binding (0.82, 9.0E−5, 6.4E−2); zinc-finger (0.82,



1.7E−3, 1.9E−1); zinc (0.82, 2.3E−3, 2.1E−1);



ribonucleoprotein (0.69, 1.5E−4, 5.5E−2); ribosomal



protein (0.69, 8.3E−4, 1.4E−1); protease (0.62, 1.7E−2,



6.2E−1); kinase (0.32, 7.0E−3, 3.7E−1); transferase (0.32,



1.8E−2, 6.0E−1);


327
nuclear protein (1.74, 1.0E−3, 3.2E−1); transcription

a
a
g



(1.74, 4.8E−3, 5.1E−1); dna-binding (1.74, 5.5E−3, 4.9E−1);
A %
81.34
58.40
11.62



transport (1.48, 7.6E−4, 4.3E−1); gtp-binding (1.28,
T %
9.785
0.917
1.529



3.0E−3, 5.2E−1);
G %
3.669
30.58
84.40




C %
5.198
10.09
2.446


306
transit peptide (1.44, 9.2E−3, 6.2E−1); transcription

t
t
g



regulation (1.43, 8.5E−3, 6.5E−1); dna-binding (0.71,
A %
0
30.39
11.11



8.6E−5, 6.1E−2); transcription regulation (0.71, 8.5E−3,
T %
59.80
40.52
15.03



6.5E−1); transcription regulation (0.69, 8.5E−3, 6.5E−1);
G %
4.248
15.68
45.75




C %
35.94
13.39
28.10


305
multigene family (5.69, 1.4E−9, 1.0E−6); signal (5.69,

a
a
t



5.1E−7, 1.9E−4); toxin (3.16, 8.9E−5, 1.3E−2); plant toxin
A %
72.78
66.55
27.86



(3.16, 8.9E−5, 1.3E−2); plant defense (3.16, 3.0E−3, 1.7E−1);
T %
5.245
1.639
36.06



membrane (2.9, 5.1E−5, 9.3E−3); transmembrane (2.9,
G %
9.180
15.40
11.80



2.4E−4, 2.5E−2); calcium (1.69, 3.3E−4, 3.0E−2); iron
C %
12.78
16.39
24.26



(1.69, 5.9E−4, 4.6E−2); oxidoreductase (1.69, 1.1E−3,



7.6E−2); metal-binding (1.69, 2.3E−3, 1.4E−1); hydrogen



peroxide (1.69, 3.1E−3, 1.6E−1);


305
cytoplasm (1.72, 1.3E−4, 5.5E−2); chloroplast (1.72, 1.0E−2,

g
t
a



5.9E−1); nuclear protein (1.31, 1.0E−2, 5.7E−1);
A %
26.22
30.16
47.54



transmembrane (1.27, 2.8E−3, 2.6E−1); ribosomal protein
T %
21.96
32.78
28.52



(1.05, 4.8E−4, 8.4E−2); ribonucleoprotein (1.05, 7.4E−4,
G %
27.86
12.45
5.573



1.0E−1); cytosolic ribosome (sensu Eukaryota) (1.05,
C %
23.93
24.59
18.36



7.7E−3, 6.7E−1); eukaryotic 43S preinitiation complex



(1.05, 9.2E−3, 6.3E−1); metal-binding (1.01, 1.5E−2, 6.6E−1);



transmembrane (0.89, 2.8E−3, 2.6E−1);


302
chloroplast (5.22, 5.5E−9, 2.4E−6); plastid (5.22, 8.4E−9,

t
c
t



1.8E−6); cytoplasm (5.22, 9.7E−9, 1.4E−6); membrane-
A %
6.622
1.986
22.51



bound organelle (5.22, 1.4E−5, 1.5E−3); intracellular
T %
70.52
5.960
64.90



membrane-bound organelle (5.22, 2.0E−5, 1.7E−3);
G %
8.609
4.635
7.947



organelle (5.22, 6.8E−5, 4.9E−3);
C %
14.23
87.41
4.635


245
plastid (1.18, 5.2E−3, 6.8E−1); cytoplasm (1.18, 5.9E−3,

t
t
t



5.7E−1);
A %
11.42
2.857
19.59




T %
66.12
91.02
49.38




G %
8.571
3.673
13.06




C %
13.87
2.448
17.95


242
chloroplast (2.61, 3.6E−6, 1.6E−3); plastid (2.61, 4.8E−6,

t
c
t



1.0E−3); cytoplasm (2.61, 1.5E−3, 2.0E−1); membrane-
A %
12.80
2.066
17.76



bound organelle (2.61, 6.5E−3, 5.1E−1); intracellular
T %
55.37
18.59
78.92



membrane-bound organelle (2.61, 9.0E−3, 5.4E−1);
G %
15.28
5.785
0.826



transcription (2.01, 2.1E−3, 4.0E−1); transcription
C %
16.52
73.55
2.479



regulation (2.01, 2.6E−3, 3.8E−1); nuclear protein (2.01,
A %
4.366
2.620
5.240



1.7E−2, 6.8E−1); gpi-anchor (1.76, 2.7E−4, 1.8E−1);
T %
93.88
3.930
83.40



lipoprotein (1.76, 2.1E−3, 5.3E−1); glycoprotein (1.76,
G %
0
5.240
0.873



5.6E−3, 4.9E−1); membrane (1.76, 5.7E−3, 4.5E−1); signal
C %
1.746
88.20
10.48



(1.76, 8.5E−3, 4.6E−1); anchored to membrane (1.76,



1.4E−2, 6.3E−1); nuclease (1.05, 8.0E−3, 4.8E−1);



membrane (0.93, 5.7E−3, 4.5E−1);


219
membrane (2.87, 6.1E−7, 4.5E−4); transmembrane (2.87,

a
a
a



1.9E−3, 1.8E−1); transport (2.87, 5.4E−3, 3.9E−1); signal
A %
51.59
94.06
51.59



(2.27, 3.2E−6, 7.8E−4); glycoprotein (2.27, 4.9E−4, 6.9E−2);
T %
10.50
1.369
10.50



cell wall (sensu Magnoliophyta) (1.5, 2.0E−3, 2.5E−1);
G %
17.35
4.109
23.28



cell wall (1.5, 1.0E−2, 6.7E−1); external encapsulating
C %
20.54
0.456
14.61



structure (1.5, 1.1E−2, 6.2E−1); metal-binding (0.97, 1.1E−3,



1.2E−1); transport (0.68, 5.4E−3, 3.9E−1); coiled coil



(0.21, 1.4E−2, 6.8E−1);


196
transcription (2.65, 7.7E−4, 4.3E−1); transcription

c
a
c



regulation (2.65, 9.4E−4, 2.9E−1); nuclear protein (2.65,
A %
18.36
53.57
21.42



2.4E−3, 4.4E−1); plastid (1.56, 1.0E−2, 6.5E−1);
T %
7.653
36.22
23.97




G %
29.59
5.102
26.02




C %
44.38
5.102
28.57


187
membrane (1.5, 1.6E−3, 6.9E−1); transmembrane (1.5,

g
a
t



7.5E−3, 6.7E−1); chaperone (1.23, 6.3E−3, 6.9E−1);
A %
35.82
44.91
10.16




T %
1.604
43.85
73.26




G %
50.26
4.812
1.069




C %
12.29
6.417
15.50


176
transit peptide (2.61, 1.9E−5, 1.4E−2); lyase (2.61, 1.4E−4,

g
a
a



4.9E−2); Ribulose bisphosphate carboxylase, small chain
A %
14.20
88.06
92.61



(2.61, 1.6E−4, 4.7E−1); carbon dioxide fixation (2.61,
T %
2.840
1.704
0.568



4.8E−4, 1.1E−1); photorespiration (2.61, 6.3E−4, 1.1E−1);
G %
81.81
7.954
6.25



photosynthesis (2.61, 1.2E−3, 1.6E−1); chloroplast (2.61,
C %
1.136
2.272
0.568



1.7E−3, 1.8E−1); GLYOXYLATE AND



DICARBOXYLATE METABOLISM (2.61, 2.9E−3,



2.8E−1); multigene family (2.61, 4.1E−3, 3.1E−1); plastid



(2.61, 4.6E−3, 3.1E−1); cytoplasm (1.35, 1.1E−3, 1.5E−1);


165
nuclear protein (1.99, 7.5E−4, 4.2E−1); chloroplast (1.58,

c
t
t



4.7E−3, 6.8E−1); nuclear protein (0.59, 7.5E−4, 4.2E−1);
A %
9.090
4.848
4.242




T %
24.84
90.30
89.69




G %
6.060
3.636
1.818




C %
60
1.212
4.242


162
metal-binding (1.1, 6.8E−4, 3.9E−1); zinc (0.62, 2.5E−3,

t
g
a



6.0E−1); kinase (0.61, 4.4E−3, 6.6E−1);
A %
31.48
17.90
69.75




T %
43.20
24.69
10.49




G %
12.96
48.14
15.43




C %
12.34
9.259
4.320


161
dna-binding (2.13, 1.2E−3, 5.7E−1); nuclear protein (2.13,

t
t
a



2.0E−3, 5.1E−1);
A %
19.87
26.08
50.93




T %
73.29
45.96
32.91




G %
3.105
3.105
10.55




C %
3.726
24.84
5.590


160
membrane (1.72, 3.9E−4, 2.5E−1); plastid (0.77, 2.6E−3,

t
c
t



6.7E−1); chloroplast (0.77, 4.7E−3, 6.4E−1);
A %
11.87
11.25
0.625




T %
78.75
23.75
96.87




G %
6.25
6.25
1.875




C %
3.125
58.75
0.625


157
chloroplast (2.62, 2.0E−4, 8.3E−2); plastid (2.62, 2.4E−4,

a
a
g



5.1E−2); membrane-bound organelle (2.62, 7.8E−4, 1.1E−1);
A %
64.96
59.23
31.84



intracellular membrane-bound organelle (2.62, 1.3E−3,
T %
12.73
5.732
6.369



1.3E−1); organelle (2.62, 2.0E−3, 1.6E−1); cytoplasm
G %
8.917
28.66
36.30



(2.62, 2.7E−3, 1.8E−1); intracellular organelle (2.62, 3.3E−3,
C %
13.37
6.369
25.47



1.8E−1); intracellular (2.62, 7.6E−3, 3.4E−1);


155
ubiquitin-protein ligase activity (1.21, 1.2E−3, 6.4E−1);

g
a
t




A %
18.06
35.48
3.225




T %
25.80
29.03
89.67




G %
38.06
21.93
6.451




C %
18.06
13.54
0.645


152
transmembrane (1.61, 3.1E−3, 5.3E−1);

t
t
g



glycosyltransferase (1.11, 5.3E−3, 6.3E−1); metal-binding
A %
3.947
15.78
15.13



(0.47, 8.1E−4, 4.5E−1);
T %
94.07
42.10
3.289




G %
1.973
3.289
46.71




C %
0
38.81
34.86


150
membrane (1.9, 1.3E−3, 6.1E−1); membrane (1.34, 1.3E−3,

t
t
a



6.1E−1); nucleotide-binding (0.44, 1.9E−3, 5.1E−1);
A %
2
9.333
35.33




T %
97.33
48.66
27.33




G %
0.666
18.66
27.33




C %
0
23.33
10


139
ribosomal protein (2.22, 9.5E−6, 7.0E−3); intracellular

c
c
g



non-membrane-bound organelle (2.22, 1.1E−5, 4.6E−3);
A %
15.10
1.438
0



non-membrane-bound organelle (2.22, 1.1E−5, 4.6E−3);
T %
26.61
0
2.877



ribonucleoprotein complex (2.22, 1.1E−5, 1.6E−3);
G %
2.158
0
96.40



ribosome (2.22, 1.1E−4, 1.2E−2); structural constituent of
C %
56.11
98.56
0.719



ribosome (2.22, 1.5E−4, 2.2E−1); structural molecule



activity (2.22, 2.2E−4, 1.7E−1); ribonucleoprotein (2.22,



2.9E−4, 1.0E−1); ribosome (2.22, 6.0E−3, 6.7E−1);



RIBOSOME (2.22, 6.7E−3, 5.3E−1); ribosomal protein



(2.21, 9.5E−6, 7.0E−3); RIBOSOME (2.21, 6.7E−3, 5.3E−1);


131
threonine protease (2.08, 7.9E−4, 4.4E−1);

a
a
t




A %
70.22
96.18
35.11




T %
6.870
1.526
45.03




G %
17.55
1.526
12.97




C %
5.343
0.763
6.870


120
wd repeat (2.32, 1.9E−4, 1.3E−1); WD40 (2.32, 2.1E−3,

a
t
c



5.2E−1); transferase (0.68, 1.9E−3, 5.0E−1);
A %
46.66
11.66
10.83




T %
14.16
37.5
18.33




G %
34.16
14.16
17.5




C %
5
36.66
53.33


117
metal-binding (1.95, 5.6E−4, 3.4E−1); nuclear protein

a
t
c



(1.46, 1.7E−3, 4.6E−1); signal (1.15, 2.3E−3, 4.3E−1);
A %
66.66
5.128
21.36




T %
17.09
65.81
4.273




G %
6.837
21.36
0.854




C %
9.401
7.692
73.50


109
intracellular (1.56, 4.3E−3, 6.1E−1);

g
c
g




A %
27.52
14.67
20.18




T %
21.10
19.26
15.59




G %
37.61
5.504
64.22




C %
13.76
60.55
0


108
chloroplast (4.2, 6.9E−6, 3.0E−3); plastid (4.2, 8.5E−6,

t
c
t



1.8E−3); intracellular membrane-bound organelle (4.2,
A %
4.629
1.851
12.96



3.3E−5, 4.8E−3); membrane-bound organelle (4.2, 3.8E−5,
T %
71.29
14.81
62.03



4.1E−3); intracellular organelle (4.2, 6.5E−5, 5.6E−3);
G %
20.37
15.74
22.22



intracellular (4.2, 6.7E−5, 4.8E−3); organelle (4.2, 7.4E−5,
C %
3.703
67.59
2.777



4.5E−3); cytoplasm (4.2, 2.0E−4, 1.1E−2); cell (4.2, 3.2E−3,



1.4E−1); OXIDATIVE PHOSPHORYLATION (0.79,



6.7E−3, 5.3E−1);


104
response to abiotic stimulus (3.87, 2.9E−6, 6.0E−3);

t
c
t



response to stimulus (3.87, 6.4E−5, 6.3E−2);
A %
5.769
4.807
36.53




T %
83.65
3.846
40.38




G %
6.730
2.884
22.11




C %
3.846
88.46
0.961


100
transit peptide (1.65, 2.9E−3, 4.2E−1); metal-binding

t
c
t



(1.43, 6.7E−3, 6.2E−1); ribonucleoprotein (0.96, 7.5E−4,
A %
19
3
8



4.2E−1); ribosomal protein (0.96, 1.9E−3, 5.1E−1); metal-
T %
42
7
90



binding (0.44, 6.7E−3, 6.2E−1);
G %
31
5
0




C %
8
85
2


93
multigene family (3.38, 1.7E−6, 1.3E−3); calmodulin-

g
t
t



binding (3.38, 1.1E−5, 3.9E−3); membrane (3.38, 7.5E−4,
A %
17.20
16.12
0



8.8E−2); transmembrane (3.38, 7.0E−3, 4.7E−1); zinc
T %
17.20
54.83
98.92



(2.79, 2.9E−4, 5.2E−2); alternative splicing (2.79, 7.3E−4,
G %
50.53
25.80
0



1.0E−1); metal-binding (1.19, 8.2E−5, 2.0E−2); zinc (1.19,
C %
15.05
3.225
1.075



2.9E−4, 5.2E−2); zinc-finger (1.19, 1.1E−3, 1.1E−1);


85
intracellular membrane-bound organelle (3.4, 5.0E−5,

t
c
t



2.1E−2); membrane-bound organelle (3.4, 5.6E−5, 1.2E−2);
A %
4.705
3.529
20



cytoplasm (3.4, 2.0E−4, 2.8E−2); intracellular
T %
91.76
2.352
77.64



organelle (3.4, 2.0E−4, 2.1E−2); organelle (3.4, 2.2E−4,
G %
0
1.176
2.352



1.9E−2); intracellular (3.4, 1.8E−3, 1.2E−1); cytoplasm
C %
3.529
92.94
0



(2.65, 2.0E−4, 2.8E−2); chloroplast (2.65, 7.3E−3, 3.3E−1);



plastid (2.65, 8.0E−3, 3.2E−1); TIR (1.04, 6.1E−3, 6.6E−1);


81
lipid biosynthesis (1.91, 5.5E−4, 6.7E−1);

a
a
a




A %
44.44
75.30
95.06




T %
20.98
20.98
1.234




G %
30.86
3.703
3.703




C %
3.703
0
0


67
zinc-finger (1.22, 9.0E−4, 4.8E−1); zinc (1.22, 1.8E−3,

c
a
t



4.9E−1);
A %
22.38
52.23
13.43




T %
16.41
38.80
85.07




G %
26.86
8.955
1.492




C %
34.32
0
0


67
envelope (1.09, 4.6E−3, 6.4E−1);

c
a
t




A %
44.77
71.64
7.462




T %
4.477
17.91
88.05




G %
2.985
4.477
1.492




C %
47.76
5.970
2.985


61
TERPENOID BIOSYNTHESIS (2.15, 3.9E−3, 3.6E−1);

c
g
a



BIOSYNTHESIS OF STEROIDS (2.15, 1.5E−2, 5.8E−1);
A %
8.196
4.918
59.01




T %
18.03
6.557
34.42




G %
22.95
70.49
4.918




C %
50.81
18.03
1.639


54
RNA POLYMERASE (2.11, 1.9E−3, 1.9E−1);

t
a
g



PYRIMIDINE METABOLISM (2.11, 1.3E−2, 5.3E−1);
A %
1.851
55.55
14.81



PURINE METABOLISM (2.11, 1.8E−2, 5.0E−1);
T %
79.62
40.74
3.703




G %
16.66
1.851
81.48




C %
1.851
1.851
0


52
ribonucleoprotein (0.95, 8.9E−4, 2.8E−1);

t
c
t




A %
15.38
0
5.769




T %
59.61
0
67.30




G %
13.46
0
3.846




C %
11.53
100
23.07


47
transport (1.34, 2.0E−4, 1.4E−1);

g
a
a




A %
0
89.36
87.23




T %
0
0
0




G %
100
2.127
12.76




C %
0
8.510
0


46
cell (1.99, 5.3E−3, 6.9E−1); plastid (1.99, 5.6E−3, 5.6E−1);

t
c
g



intracellular organelle (1.99, 9.8E−3, 4.6E−1); organelle
A %
23.91
8.695
8.695



(1.99, 1.0E−2, 4.3E−1); intracellular (1.99, 1.1E−2, 4.0E−1);
T %
41.30
10.86
10.86



intracellular membrane-bound organelle (1.99, 1.5E−2,
G %
15.21
2.173
67.39



4.8E−1); membrane-bound organelle (1.99, 1.5E−2,
C %
19.56
78.26
13.04



4.6E−1); cytoplasm (1.99, 3.3E−2, 6.7E−1); membrane-



enclosed lumen (1.37, 5.8E−3, 3.9E−1); organelle lumen



(1.37, 5.8E−3, 3.9E−1); nucleolus (1.37, 9.4E−3, 4.9E−1);



nuclear lumen (1.37, 2.6E−2, 6.1E−1);


43
heat shock (2.56, 1.4E−3, 4.0E−1);

t
a
a




A %
4.651
90.69
65.11




T %
53.48
0
6.976




G %
13.95
4.651
23.25




C %
27.90
4.651
4.651


43
eukaryotic 43S preinitiation complex (1.5, 2.9E−5, 1.3E−2);

t
t
t



cytosolic small ribosomal subunit (sensu Eukaryota)
A %
4.651
0
0



(1.5, 1.0E−3, 1.4E−1); eukaryotic 48S initiation complex
T %
81.39
58.13
100



(1.5, 1.0E−3, 1.4E−1); protein complex (1.5, 2.0E−3, 1.9E−1);
G %
4.651
2.325
0



small ribosomal subunit (1.5, 3.1E−3, 2.3E−1);
C %
9.302
39.53
0



cytosolic ribosome (sensu Eukaryota) (1.5, 5.2E−3, 3.1E−1);


42
disulfide bond (1.35, 1.5E−3, 6.9E−1);

g
a
g




A %
2.380
88.09
11.90




T %
21.42
4.761
0




G %
66.66
2.380
80.95




C %
9.523
4.761
7.142


42
transcription regulation (1.4, 4.2E−3, 6.5E−1); nuclear

a
a
a



protein (1.4, 5.5E−3, 6.4E−1); metal-binding (1.4, 6.5E−3,
A %
95.23
38.09
88.09



6.2E−1); nuclear protein (0.47, 5.5E−3, 6.4E−1);
T %
2.380
14.28
7.142




G %
0
26.19
4.761




C %
2.380
21.42
0


40
atp-binding (1.01, 1.5E−3, 6.6E−1); nucleotide-binding

gc
t
c



(1.01, 2.2E−3, 5.5E−1);
A %
15
0
10




T %
10
95
0




G %
37.5
0
2.5




C %
37.5
5
87.5


36
cytoplasm (2.29, 3.6E−4, 1.4E−1); mitochondrion (2.29,

tg
a
c



5.2E−4, 1.1E−1); intracellular membrane-bound organelle
A %
0
72.22
0



(2.29, 4.7E−3, 4.9E−1); membrane-bound organelle (2.29,
T %
38.88
0
0



4.9E−3, 4.1E−1); intracellular organelle (2.29, 8.7E−3,
G %
38.88
27.77
0



4.7E−1); organelle (2.29, 9.1E−3, 4.3E−1); intracellular
C %
22.22
0
100



(2.29, 2.3E−2, 6.1E−1); ribosome (0.87, 7.8E−3, 4.9E−1);



non-membrane-bound organelle (0.87, 1.1E−2, 4.1E−1);



intracellular non-membrane-bound organelle (0.87, 1.1E−2,



4.1E−1); ribonucleoprotein complex (0.87, 1.9E−2, 5.6E−1);


35
chloroplast stroma (1.04, 1.1E−3, 3.9E−1); plastid stroma

g
ag
t



(1.04, 2.1E−3, 3.7E−1);
A %
40
40
11.42




T %
2.857
2.857
88.57




G %
48.57
40
0




C %
8.571
17.14
0


35
membrane (1.78, 4.1E−6, 3.0E−3); transmembrane (1.78,

g
a
c



4.9E−5, 1.8E−2); transmembrane region (1.78, 7.3E−4,
A %
11.42
34.28
0



4.3E−1); ubl conjugation pathway (1.78, 1.4E−3, 2.8E−1);
T %
28.57
31.42
0



metal-binding (1.78, 2.0E−3, 3.0E−1); zinc (1.78, 5.1E−3,
G %
34.28
22.85
0



5.2E−1);
C %
25.71
11.42
100


34
transcription factor activity (1.03, 2.5E−4, 3.3E−1);

t
t
c



transcription regulator activity (1.03, 7.7E−4, 4.7E−1);
A %
0
0
0




T %
94.11
94.11
5.882




G %
0
5.882
2.941




C %
5.882
0
91.17


32
prenylation (2.78, 3.3E−5, 2.4E−2); lipid moiety-binding

a
c
g



region: S-geranylgeranyl cysteine (2.78, 1.0E−4, 7.5E−2);
A %
62.5
6.25
3.125



lipoprotein (2.78, 4.9E−4, 1.6E−1); nucleotide phosphate-
T %
0
0
9.375



binding region: GTP (2.78, 1.4E−3, 4.1E−1); gtp-binding
G %
34.37
0
84.37



(2.78, 2.0E−3, 3.9E−1); membrane (2.78, 4.7E−3, 5.8E−1);
C %
3.125
93.75
3.125


32
membrane (2.21, 8.0E−6, 5.9E−3); transmembrane (2.21,

g
ag
c



9.5E−5, 3.4E−2); metal-binding (2.21, 2.6E−4, 6.2E−2);
A %
12.5
37.5
0



zinc (2.21, 5.2E−4, 9.1E−2); transmembrane region (2.21,
T %
25
12.5
0



7.3E−4, 4.3E−1); ubl conjugation pathway (2.21, 1.7E−3,
G %
56.25
37.5
0



2.2E−1); zinc-finger (2.21, 4.5E−3, 4.2E−1);
C %
6.25
12.5
100


28
SF016605: Arabidopsis thaliana transcription factor

c
t
c



DREB1B (2.02, 2.8E−5, 9.8E−2); DNA-binding
A %
10.71
0
0



region: AP2/ERF (2.02, 9.4E−5, 7.0E−2); transcription
T %
39.28
85.71
28.57



factor (2.02, 2.7E−4, 1.8E−1); activator (2.02, 8.7E−4,
G %
7.142
14.28
14.28



2.7E−1); nuclear protein (2.02, 1.6E−3, 3.3E−1);
C %
42.85
0
57.14


28
nuclear protein (3.28, 8.0E−5, 5.7E−2); transcription

t
t
t



(3.28, 2.0E−4, 7.1E−2); transcription regulation (3.28,
A %
0
0
3.571



2.2E−4, 5.3E−2);
T %
53.57
100
96.42




G %
17.85
0
0




C %
28.57
0
0


27
response to water deprivation (1.91, 3.3E−4, 4.9E−1);

c
t
t



response to water (1.91, 5.0E−4, 4.0E−1);
A %
0
0
14.81




T %
0
96.29
51.85




G %
7.407
3.703
29.62




C %
92.59
0
3.703


26
response to chemical stimulus (2.9, 3.0E−4, 4.6E−1);

a
a
c



response to hormone stimulus (2.9, 6.2E−4, 4.7E−1);
A %
84.61
80.76
15.38



response to abiotic stimulus (2.9, 9.7E−4, 4.8E−1);
T %
11.53
19.23
3.846




G %
3.846
0
19.23




C %
0
0
61.53


26
nucleotide-binding (1.12, 2.2E−3, 5.5E−1); transferase

t
t
g



(1.12, 2.7E−3, 4.9E−1);
A %
0
0
0




T %
92.30
88.46
19.23




G %
7.692
0
69.23




C %
0
11.53
11.53


25
ubiquitin conjugating enzyme activity (1.05, 2.4E−4,

c
t
c



3.3E−1); small protein conjugating enzyme activity (1.05,
A %
0
4
4



2.8E−4, 2.0E−1); UBCc (1.05, 1.7E−3, 4.5E−1);
T %
32
92
0




G %
8
4
0




C %
60
0
96


25
nuclear protein (2.56, 1.0E−3, 5.2E−1); transcription

t
t
t



regulation (2.56, 4.7E−3, 6.9E−1);
A %
0
0
4




T %
56
100
96




G %
20
0
0




C %
24
0
0


25
Protein phosphatase 2C (2, 2.3E−4, 6.0E−1); PP2Cc (2,

a
g
a



3.2E−3, 6.8E−1);
A %
96
16
100




T %
0
0
0




G %
0
80
0




C %
4
4
0


24
pyridoxal phosphate (3.68, 9.5E−7, 7.0E−4);

t
g
t



nicotianamine synthase activity (3.68, 1.7E−6, 2.9E−3);
A %
20.83
0
0



Nicotianamine synthase (3.68, 2.0E−6, 8.1E−3); multigene
T %
45.83
16.66
100



family (3.68, 1.1E−3, 3.4E−1); transferase activity,
G %
0
62.5
0



transferring alkyl or aryl (other than methyl) groups
C %
33.33
20.83
0



(3.68, 1.4E−3, 6.8E−1);













Size of Cluster
Distribution of nucleotides per position



(number of context
along the context sequence (%)















sequences)
−6
−5
−4
−3
−2
−1







1613
a
a
a
a
a
a




61.50
74.27
73.03
89.77
79.54
71.48




3.967
4.091
1.735
1.735
2.603
7.873




28.58
6.943
23.49
7.501
6.137
15.93




5.951
14.69
1.735
0.991
11.71
4.711



1433
t
t
a
a
a
a




19.05
29.09
73.83
65.10
57.50
50.03




46.12
33.63
9.141
8.374
10.81
12.63




24.49
23.23
10.53
23.86
3.838
23.16




10.32
14.02
6.489
2.651
27.84
14.16



1345
a
a
g
a
a
a




42.08
41.48
26.54
72.26
73.53
49.07




30.85
29.07
12.93
1.040
9.293
5.204




14.20
12.56
51.59
24.83
12.11
31.15




12.86
16.87
8.921
1.858
5.055
14.57



751
a
a
a
a
c
a




77.36
38.88
94.67
84.68
32.75
79.62




6.125
1.731
0.665
5.592
2.263
2.396




12.91
31.29
2.396
7.856
9.986
11.05




3.595
28.09
2.263
1.864
54.99
6.924



680
g
a
g
a
a
a




23.38
44.11
8.382
91.17
48.23
77.5




20.58
27.79
7.941
2.794
34.11
6.470




34.70
5.882
66.91
3.676
11.17
12.94




21.32
22.20
16.76
2.352
6.470
3.088



680
t
c
a
g
c
a




8.088
6.323
51.61
24.11
36.17
62.20




74.11
42.35
26.91
18.67
7.058
10.88




11.61
3.235
5.147
47.94
9.117
8.970




6.176
48.08
16.32
9.264
47.64
17.94



655
t
c
t
t
c
a




4.122
5.496
9.770
8.396
14.80
52.97




81.37
24.27
69.31
34.96
30.99
7.328




10.83
11.29
6.870
23.66
3.816
9.465




3.664
58.93
14.04
32.97
50.38
30.22



618
c
a
a
a
c
a




10.51
44.17
80.09
72.00
9.385
59.87




15.37
22.00
3.883
19.41
17.31
7.766




12.94
5.177
11.00
7.443
5.987
7.443




61.16
28.64
5.016
1.132
67.31
24.91



462
a
g
a
g
a
a




93.07
5.411
95.45
20.34
89.39
41.12




5.844
1.731
2.380
1.731
1.298
18.83




0
88.52
1.731
75.32
3.896
35.93




1.082
4.329
0.432
2.597
5.411
4.112



457
g
a
a
a
a
a




12.03
75.92
65.86
50.98
52.29
53.61




1.750
4.814
14.66
10.06
7.877
12.91




84.68
2.625
15.97
29.32
8.752
13.34




1.531
16.63
3.501
9.628
31.07
20.13



375
a
t
c
a
c
c




77.06
24.26
1.866
62.93
5.866
13.06




14.93
54.4
5.6
9.6
30.93
12.26




4.266
1.333
2.133
24.53
1.333
8.8




3.733
20
90.4
2.933
61.86
65.86



327
a
a
g
a
a
g




93.57
85.32
1.529
90.82
70.94
11.31




2.446
0.305
0.611
0.305
6.727
3.975




1.834
9.785
96.94
8.562
1.834
82.56




2.140
4.587
0.917
0.305
20.48
2.140



306
a
a
a
a
a
a




84.96
55.22
88.56
93.13
83.66
66.66




3.921
16.01
1.633
0.653
1.633
5.228




1.307
14.70
4.248
3.921
2.941
19.28




9.803
14.05
5.555
2.287
11.76
8.823



305
c
a
a
a
a
a




24.91
77.37
92.45
96.06
62.29
42.95




4.262
4.262
2.622
0
26.55
12.78




0.327
10.16
2.295
2.950
6.557
9.508




70.49
8.196
2.622
0.983
4.590
34.75



305
t
c
a
a
t
c




15.40
23.93
78.03
68.19
19.67
1.967




67.21
19.01
1.311
7.540
57.04
1.967




8.196
5.245
9.508
16.39
1.967
0.983




9.180
51.80
11.14
7.868
21.31
95.08



302
t
c
a
t
c
a




1.655
1.324
40.72
19.20
0.662
66.88




60.92
0.993
27.81
44.70
2.649
3.311




9.602
2.649
29.47
28.47
0
18.54




27.81
95.03
1.986
7.615
96.68
11.25



245
t
c
a
a
a
a




22.85
6.530
74.69
85.30
90.61
74.28




55.91
22.85
3.673
0.408
3.265
1.632




18.36
28.16
18.77
11.42
3.265
22.44




2.857
42.44
2.857
2.857
2.857
1.632



242
t
c
a
t
c
a




3.305
1.239
47.93
18.18
0
85.95




72.72
2.066
42.14
72.72
2.066
4.958




8.264
2.892
9.090
2.479
0
4.132




15.70
93.80
0.826
6.611
97.93
4.958




17.90
7.860
17.03
16.59
20.08
24.01




13.97
83.40
36.24
50.21
11.35
17.03




24.89
0.873
3.056
27.51
6.550
23.14




43.23
7.860
43.66
5.676
62.00
35.80



219
a
t
c
a
a
a




82.19
34.70
2.283
97.71
95.89
70.31




5.936
39.26
2.739
0
0.913
17.35




2.739
11.41
7.762
0.913
0.913
2.739




9.132
14.61
87.21
1.369
2.283
9.589



196
t
c
t
c
t
a




10.20
5.102
2.040
3.061
8.673
37.24




58.67
29.59
93.87
10.20
65.30
18.36




8.673
16.32
1.020
21.93
4.081
29.08




22.44
48.97
3.061
64.79
21.93
15.30



187
t
a
g
a
a
g




6.951
42.24
29.94
88.77
99.46
3.208




41.71
9.625
4.278
1.069
0
0.534




32.08
8.021
60.42
4.812
0
93.58




19.25
40.10
5.347
5.347
0.534
2.673



176
g
a
a
g
a
a




1.704
71.59
87.5
1.136
58.52
39.20




1.704
7.386
1.704
2.272
15.34
8.522




96.02
13.63
6.818
96.59
2.272
25




0.568
7.386
3.977
0
23.86
27.27



165
c
t
t
t
c
ac




2.424
9.696
3.030
10.90
9.090
32.12




31.51
62.42
55.15
44.84
36.36
5.454




2.424
3.030
0.606
19.39
5.454
30.30




63.63
24.84
41.21
24.84
49.09
32.12



162
g
t
t
t
t
a




24.07
17.90
8.641
1.851
7.407
38.88




8.641
40.74
85.80
88.88
57.40
8.024




64.19
17.28
3.703
8.024
3.703
32.71




3.086
24.07
1.851
1.234
31.48
20.37



161
g
c
a
g
a
g




26.08
17.39
47.20
43.47
93.78
3.105




1.242
2.484
9.937
8.074
4.968
1.863




47.82
3.105
34.16
48.44
1.242
65.21




24.84
77.01
8.695
0
0
29.81



160
c
t
a
a
a
a




3.125
13.12
33.75
74.37
51.25
94.37




3.125
53.12
12.5
13.12
4.375
0.625




1.25
3.125
25
5.625
9.375
3.75




92.5
30.62
28.75
6.875
35
1.25



157
a
t
t
c
a
g




57.32
26.11
1.273
1.273
64.96
29.93




35.66
50.95
98.72
14.64
4.458
9.554




5.095
3.821
0
8.917
0.636
56.05




1.910
19.10
0
75.15
29.93
4.458



155
t
t
t
g
a
a




0
1.290
7.096
3.225
77.41
67.74




90.96
92.90
49.03
1.935
12.90
13.54




1.935
2.580
27.09
90.96
1.935
14.19




7.096
3.225
16.77
3.870
7.741
4.516



152
t
t
c
a
a
a




3.947
19.73
11.18
46.05
69.07
61.18




78.94
64.47
18.42
14.47
23.02
7.894




7.894
9.868
30.26
29.60
4.605
21.05




9.210
5.921
40.13
9.868
3.289
9.868



150
g
t
g
a
c
g




10
28.66
1.333
71.33
25.33
22.66




0.666
50
29.33
2
19.33
28




81.33
8.666
48.66
20
11.33
36.66




8
12.66
20.66
6.666
44
12.66



139
g
c
g
a
a
a




23.02
23.02
16.54
80.57
60.43
67.62




4.316
6.474
0.719
7.913
17.26
15.10




69.78
2.877
79.13
10.07
9.352
13.66




2.877
67.62
3.597
1.438
12.94
3.597



131
c
t
g
a
a
a




25.19
7.633
0.763
82.44
94.65
61.06




31.29
51.90
3.053
1.526
0
9.923




11.45
37.40
93.12
13.74
2.290
21.37




32.06
3.053
3.053
2.290
3.053
7.633



120
g
g
a
a
a
a




19.16
3.333
95
88.33
46.66
70




14.16
0.833
0.833
5.833
23.33
4.166




51.66
95
2.5
5
14.16
7.5




15
0.833
1.666
0.833
15.83
18.33



117
a
t
c
a
t
c




75.21
0.854
5.982
88.88
3.418
0




12.82
92.30
3.418
2.564
70.94
0.854




7.692
0
0.854
3.418
0
0




4.273
6.837
89.74
5.128
25.64
99.14



109
a
c
g
g
c
g




61.46
3.669
0.917
40.36
37.61
8.256




3.669
5.504
2.752
1.834
0.917
2.752




29.35
0
96.33
55.96
0
85.32




5.504
90.82
0
1.834
61.46
3.669



108
t
g
a
g
t
g




12.96
9.259
83.33
0
25
43.51




85.18
25
3.703
1.851
39.81
11.11




1.851
56.48
8.333
97.22
5.555
44.44




0
9.259
4.629
0.925
29.62
0.925



104
g
a
a
a
a
a




0.961
93.26
86.53
97.11
90.38
69.23




32.69
3.846
3.846
0
0.961
7.692




63.46
0.961
1.923
0.961
1.923
19.23




2.884
1.923
7.692
1.923
6.730
3.846



100
t
c
g
a
a
a




9
37
1
97
86
82




66
6
1
0
0
5




21
9
72
2
5
8




4
48
26
1
9
5



93
g
a
a
g
a
a




9.677
89.24
88.17
5.376
95.69
89.24




12.90
0
5.376
2.150
1.075
4.301




48.38
9.677
5.376
86.02
0
3.225




29.03
1.075
1.075
6.451
3.225
3.225



85
c
t
t
t
c
t




7.058
2.352
4.705
17.64
17.64
29.41




4.705
95.29
60
70.58
3.529
34.11




10.58
1.176
1.176
7.058
1.176
15.29




77.64
1.176
34.11
4.705
77.64
21.17



81
a
t
c
a
c
c




88.88
32.09
2.469
39.50
7.407
9.876




3.703
59.25
1.234
22.22
9.876
8.641




1.234
2.469
2.469
33.33
1.234
27.16




6.172
6.172
93.82
4.938
81.48
54.32



67
t
t
g
g
a
a




0
0
4.477
0
91.04
62.68




68.65
98.50
5.970
1.492
4.477
29.85




28.35
0
65.67
98.50
2.985
5.970




2.985
1.492
23.88
0
1.492
1.492



67
c
a
a
t
c
c




1.492
80.59
92.53
40.29
2.985
23.88




0
4.477
4.477
47.76
2.985
5.970




0
8.955
0
11.94
0
17.91




98.50
5.970
2.985
0
94.02
52.23



61
t
a
a
g
c
c




36.06
47.54
67.21
0
0
4.918




45.90
4.918
11.47
40.98
6.557
3.278




8.196
27.86
18.03
59.01
3.278
1.639




9.836
19.67
3.278
0
90.16
90.16



54
a
c
a
a
g
g




53.70
22.22
96.29
94.44
9.259
3.703




9.259
3.703
0
3.703
0
14.81




20.37
27.77
0
0
87.03
68.51




16.66
46.29
3.703
1.851
3.703
12.96



52
t
t
a
g
c
c




26.92
0
84.61
28.84
0
5.769




34.61
86.53
0
0
1.923
1.923




3.846
11.53
1.923
67.30
0
1.923




34.61
1.923
13.46
3.846
98.07
90.38



47
g
c
a
a
t
c




6.382
36.17
68.08
93.61
0
0




2.127
0
6.382
4.255
51.06
6.382




89.36
23.40
6.382
2.127
23.40
14.89




2.127
40.42
19.14
0
25.53
78.72



46
g
t
g
g
c
c




2.173
0
26.08
0
2.173
19.56




30.43
100
2.173
2.173
10.86
6.521




58.69
0
71.73
95.65
0
21.73




8.695
0
0
2.173
86.95
52.17



43
c
t
a
a
c
a




0
2.325
97.67
95.34
0
58.13




6.976
81.39
0
0
13.95
0




16.27
6.976
0
4.651
32.55
2.325




76.74
9.302
2.325
0
53.48
39.53



43
g
t
a
a
t
c




0
20.93
67.44
95.34
32.55
0




0
37.20
0
4.651
39.53
0




100
11.62
4.651
0
0
0




0
30.23
27.90
0
27.90
100



42
a
a
a
g
t
c




92.85
42.85
97.61
7.142
0
19.04




7.142
4.761
2.380
2.380
97.61
11.90




0
40.47
0
90.47
0
7.142




0
11.90
0
0
2.380
61.90



42
t
c
t
t
g
a




9.523
2.380
33.33
0
0
95.23




78.57
4.761
57.14
97.61
26.19
0




11.90
4.761
9.523
0
40.47
2.380




0
88.09
0
2.380
33.33
2.380



40
t
t
a
g
c
c




15
0
42.5
0
0
15




80
95
27.5
7.5
0
30




5
0
17.5
92.5
0
0




0
5
12.5
0
100
55



36
g
g
a
g
a
ag




19.44
5.555
72.22
2.777
100
44.44




13.88
5.555
13.88
0
0
0




55.55
86.11
0
97.22
0
44.44




11.11
2.777
13.88
0
0
11.11



35
c
t
c
t
c
t




0
0
2.857
14.28
0
40




42.85
100
5.714
71.42
14.28
42.85




2.857
0
2.857
8.571
25.71
5.714




54.28
0
88.57
5.714
60
11.42



35
a
a
t
c
a
a




71.42
45.71
25.71
5.714
100
97.14




8.571
34.28
57.14
0
0
2.857




8.571
14.28
0
0
0
0




11.42
5.714
17.14
94.28
0
0



34
t
t
c
t
c
c




8.823
0
0
32.35
0
20.58




91.17
88.23
0
50
47.05
23.52




0
11.76
5.882
5.882
0
2.941




0
0
94.11
11.76
52.94
52.94



32
a
c
g
g
a
g




56.25
6.25
6.25
3.125
65.62
9.375




0
12.5
0
0
3.125
3.125




43.75
0
93.75
96.87
0
84.37




0
81.25
0
0
31.25
3.125



32
a
a
t
c
a
a




75
46.87
15.62
0
100
81.25




3.125
25
78.12
0
0
15.62




12.5
25
0
0
0
0




9.375
3.125
6.25
100
0
3.125



28
t
g
a
t
c
g




0
0
96.42
0
3.571
32.14




92.85
0
0
92.85
3.571
3.571




3.571
96.42
3.571
3.571
0
46.42




3.571
3.571
0
3.571
92.85
17.85



28
g
c
t
g
t
a




0
3.571
7.142
0
0
53.57




0
3.571
89.28
32.14
78.57
0




100
42.85
0
53.57
7.142
25




0
50
3.571
14.28
14.28
21.42



27
c
g
g
a
a
a




3.703
14.81
3.703
100
96.29
59.25




33.33
0
0
0
0
0




25.92
85.18
96.29
0
0
40.74




37.03
0
0
0
3.703
0



26
c
c
g
a
c
c




0
30.76
23.07
100
11.53
0




3.846
0
23.07
0
15.38
0




0
26.92
42.30
0
7.692
3.846




96.15
42.30
11.53
0
65.38
96.15



26
g
t
g
a
a
g




0
3.846
3.846
46.15
61.53
0




0
80.76
0
7.692
0
0




92.30
15.38
96.15
38.46
19.23
100




7.692
0
0
7.692
19.23
0



25
t
c
a
g
a
g




16
4
68
36
92
4




68
4
0
0
8
4




16
0
0
64
0
88




0
92
32
0
0
4



25
g
g
t
g
t
a




0
4
0
0
0
52




0
4
100
24
76
0




100
48
0
60
8
24




0
44
0
16
16
24



25
g
g
a
a
g
g




20
0
96
44
16
0




32
0
4
12
0
4




48
100
0
36
84
68




0
0
0
8
0
28



24
c
t
c
g
a
c




20.83
0
4.166
0
83.33
0




0
100
0
0
12.5
37.5




37.5
0
0
100
0
16.66




41.66
0
95.83
0
4.166
45.83

















TABLE 2





Emerging gene clusters which were identified by the clustering algorithm pertaining Homo Sapien.


The below clusters are arranged according to declining size. For each cluster, the table depicts the


distribution of nucleotides for each position along the context sequence.
















Size of Cluster










(number of

Distribution of nucleotides per position


context
Function attributes set (Enrichment
along the context sequence (%)












sequences))
score/P_value/Benjamini)
Pos:
−9
−8
−7





1562
cytoskeleton (4.63, 3.7E−7, 2.3E−4); transport (4.63, 9.3E−9,

g
c
c



2.5E−6); transporter activity (4.63, 8.4E−3, 6.2E−1);
A %
7.746
3.457
16.00



keratin (4.05, 3.0E−8, 5.9E−6); intermediate filament
T %
7.554
3.072
14.78



cytoskeleton (4.05, 7.6E−7, 2.4E−4); Keratin, high sulfur
G %
67.22
20.42
22.79



B2 protein (4.05, 2.5E−6, 1.3E−2); negative regulation of
C %
17.47
73.04
46.41



physiological process (3.46, 8.2E−5, 5.4E−2); regulation



of apoptosis (2.91, 9.7E−5, 4.6E−2); positive regulation of



apoptosis (2.91, 8.3E−4, 1.3E−1); apoptosis (2.91, 1.2E−3,



1.6E−1); developmental protein (2.76, 1.3E−4, 1.3E−2);



differentiation (2.76, 1.2E−3, 4.8E−2); anti-apoptosis



(2.71, 1.7E−2, 5.7E−1); golgi stack (2.61, 4.5E−4, 2.5E−2);



Golgi apparatus (2.61, 2.2E−3, 9.2E−2); cellular



localization (2.46, 2.4E−3, 2.1E−1); cell organization and



biogenesis (2.46, 1.2E−2, 5.0E−1); actin binding (2.44,



5.8E−4, 1.7E−1); organ morphogenesis (2.23, 6.3E−4,



1.1E−1); SF002014: carcinoembryonic antigen (1.97,



7.1E−7, 1.8E−3); pregnancy (1.97, 1.2E−4, 3.8E−2);



reproduction (1.97, 1.2E−4, 3.5E−2); pregnancy (1.97,



3.3E−4, 1.9E−2); domain: Ig-like V-type (1.97, 1.0E−3,



1.2E−1); magnesium (1.93, 1.9E−3, 6.5E−2); phosphoric



monoester hydrolase activity (1.91, 7.8E−6, 9.7E−3);



dephosphorylation (1.91, 3.9E−3, 2.9E−1); protein



phosphatase type 1 activity (1.91, 1.0E−2, 6.7E−1);



calcium-dependent protein serine/threonine phosphatase



activity (1.91, 1.1E−2, 6.9E−1); kinase (1.82, 1.6E−4,



1.5E−2); atp-binding (1.82, 2.6E−4, 1.9E−2); transferase



(1.82, 6.4E−4, 3.0E−2); purine nucleotide binding (1.82,



1.0E−3, 2.5E−1); phosphorus metabolism (1.82, 9.4E−3,



4.5E−1); adenyl nucleotide binding (1.82, 1.1E−2, 6.8E−1);



ATP (1.82, 4.9E−2, 5.4E−1); myosin (1.58, 6.5E−2, 5.6E−1);



reproduction (1.58, 1.2E−4, 3.5E−2); spermatogenesis



(1.58, 8.8E−2, 6.7E−1); protein modification (1.58, 1.3E−2,



5.2E−1); oxidoreductase activity, acting on the CH—NH2



group of donors (1.49, 3.3E−3, 4.2E−1);



domain: Ubiquitin-like (1.46, 5.7E−3, 4.8E−1); cell-matrix



junction (1.33, 3.5E−2, 4.5E−1); focal adhesion (1.33,



1.1E−1, 6.9E−1); microtubule (1.3, 1.3E−3, 5.0E−2);



microtubule (1.3, 5.6E−3, 1.7E−1); muscle protein (1.26,



2.0E−3, 6.8E−2); myofibril (1.26, 4.2E−2, 4.6E−1);



sarcomere (1.26, 1.0E−1, 6.9E−1); selenium (1.21, 6.1E−2,



5.9E−1); protease (1.2, 2.5E−3, 7.9E−2); serine protease



(1.2, 2.7E−3, 8.1E−2); initiation factor (1.15, 7.4E−2, 6.3E−1);



cholesterol metabolism (1.15, 1.3E−2, 5.2E−1); steroid



metabolism (1.15, 5.1E−2, 5.5E−1); lipid metabolism



(1.15, 5.4E−2, 5.6E−1); guanine-nucleotide releasing



factor (1.14, 4.9E−3, 1.2E−1); ruffle (1.13, 3.9E−2, 4.6E−1);



cell projection (1.13, 6.9E−2, 5.7E−1); vitamin a (1.08,



6.7E−2, 6.1E−1); secretory pathway (1.06, 2.0E−2, 6.3E−1);



iron (1.04, 5.5E−4, 2.8E−2);


987
transport (3.62, 1.8E−6, 4.9E−4); lysosome (3.03, 1.3E−4,

c
c
c



1.7E−2); lytic vacuole (3.03, 2.7E−3, 3.4E−1); intracellular
A %
5.065
2.735
17.93



signaling cascade (2.61, 5.2E−4, 3.6E−1); KRAB-related
T %
10.23
10.63
21.07



(2.49, 1.2E−7, 6.1E−4); ion transport (1.79, 7.3E−4, 7.3E−2);
G %
26.74
26.54
25.63



potassium (1.79, 2.3E−3, 1.6E−1); voltage-gated
C %
57.95
60.08
35.35



channel (1.79, 2.2E−2, 5.0E−1); differentiation (1.65,



1.1E−2, 4.0E−1); ATPase activity, coupled to



transmembrane movement of substances (1.6, 1.4E−3,



6.9E−1); hydrolase activity, acting on acid anhydrides,



catalyzing transmembrane movement of substances (1.6,



2.4E−3, 6.9E−1); atp synthesis (1.6, 6.0E−3, 2.9E−1);



hydrogen ion transport (1.6, 9.6E−3, 3.7E−1); growth



regulation (1.59, 7.1E−3, 3.1E−1); actin-binding (1.43,



6.9E−3, 3.1E−1); lipoprotein (1.39, 1.6E−2, 4.6E−1); wnt



signaling pathway (1.23, 1.7E−2, 4.6E−1); cell cycle (1.17,



4.8E−3, 2.5E−1); nucleotide-binding (1.14, 7.2E− 6, 1.4E−3);



atp-binding (1.14, 2.3E−4, 2.8E−2); transferase (1.14,



1.1E−3, 9.7E−2); prenylation (0.98, 4.9E−2, 6.9E−1);



growth factor (0.94, 2.7E−2, 5.5E−1); thick filament (0.91,



2.0E−2, 5.1E−1); muscle protein (0.91, 3.1E−2, 5.9E−1);



methylation (0.91, 4.2E−2, 6.5E−1); golgi stack (0.9, 2.6E−2,



5.4E−1); mitochondrion (0.86, 5.0E−2, 6.9E−1); cell



cycle (0.84, 4.8E−3, 2.5E−1); cell division (0.84, 2.2E−2,



5.1E−1); redox-active center (0.82, 3.3E−2, 6.1E−1);



chaperone (0.75, 5.2E−2, 6.9E−1); lipid synthesis (0.73,



1.6E−2, 4.6E−1); protein phosphatase inhibitor (0.68,



5.6E−2, 6.9E−1); aminoacyltransferase (0.62, 5.6E−2,



6.9E−1); immune response (0.31, 3.5E−2, 6.0E−1); nuclear



protein (0.29, 4.7E−2, 6.8E−1); nuclear protein (0.22,



4.7E−2, 6.8E−1);


407
response to pest, pathogen or parasite (2.79, 4.5E−5, 1.4E−1);

g
c
c



response to wounding (2.79, 8.1E−5, 1.3E−1); response
A %
26.53
10.31
5.651



to other organism (2.79, 1.1E−4, 1.2E−1); response to
T %
6.879
13.02
3.439



stress (2.79, 2.0E−4, 1.5E−1); ANTIGEN PROCESSING
G %
38.82
36.11
14.49



AND PRESENTATION (2.36, 1.2E−3, 2.1E−1);
C %
27.76
40.54
76.41



immunoglobulin domain (2.36, 3.7E−3, 3.5E−1); signal



(2.17, 6.0E−6, 8.2E−3); transmembrane (2.17, 1.0E−3,



2.1E−1); glycoprotein (2.17, 1.1E−3, 1.9E−1); Glutathione



S-transferase, Mu class (1.81, 3.4E−5, 1.6E−1); nucleotide



phosphate-binding region: PAPS (1.57, 8.6E−5, 2.9E−1);



aryl sulfotransferase activity (1.57, 6.2E−4, 5.4E−1);



sulfotransferase activity (1.57, 9.2E−4, 5.4E−1);



transferase activity, transferring sulfur-containing groups



(1.57, 1.4E−3, 5.9E−1); catecholamine metabolism (1.57,



2.2E−3, 2.9E−1); sulfotransferase (1.57, 6.5E−3, 4.9E−1);



lipid metabolism (1.57, 8.3E−3, 5.1E−1); intermediate



filament (1.47, 2.4E−3, 2.8E−1); membrane (1.35, 7.8E−5,



2.6E−2); transmembrane (1.35, 1.0E−3, 2.1E−1);



developmental protein (1.11, 8.8E−3, 5.1E−1);



transcription factor (0.85, 7.3E−3, 4.9E−1); transferase



(0.5, 1.9E−3, 2.8E−1);


398
locomotion (3.03, 9.3E−4, 6.5E−1); localization of cell

g
c
c



(3.03, 9.3E−4, 6.5E−1); cell motility (3.03, 9.3E−4, 6.5E−1);
A %
5.527
5.276
7.286



ribonucleoprotein (1.56, 2.0E−4, 8.5E−2); ribosome
T %
3.266
13.56
13.06



(1.56, 9.5E−3, 6.6E−1); RNA binding (1.47, 2.2E−4, 4.2E−1);
G %
73.61
21.10
25.37



rna-binding (1.47, 6.4E−4, 2.0E−1); cell cycle (0.91,
C %
17.58
60.05
54.27



5.5E−3, 5.6E−1); cell division (0.91, 1.1E−2, 6.7E−1);



sodium/potassium transport (0.81, 3.6E−3, 5.6E−1);



potassium transport (0.81, 7.7E−3, 6.5E−1); potassium



(0.81, 1.1E−2, 6.9E−1);


368
isomerase (1.4, 3.4E−3, 6.9E−1);

g
g
c




A %
13.31
2.445
1.902




T %
5.706
13.58
3.260




G %
55.97
77.98
17.66




C %
25
5.978
77.17


347
hormone (2.01, 2.1E−3, 4.4E−1); transport (1.83, 7.4E−4,

t
c
c



2.2E−1); signal (1.79, 5.9E−6, 4.0E−3); lipid transport
A %
30.54
2.305
6.628



(0.97, 2.2E−3, 3.9E−1); nuclear protein (0.86, 4.6E−3,
T %
32.27
11.81
11.23



5.9E−1); ubl conjugation pathway (0.79, 5.5E−3, 5.6E−1);
G %
20.74
36.88
2.305



nuclear protein (0.64, 4.6E−3, 5.9E−1); membrane (0.57,
C %
16.42
48.99
79.82



5.0E−3, 5.8E−1);


245
membrane (0.88, 2.2E−3, 5.3E−1);

g
c
c




A %
2.040
4.081
11.42




T %
1.632
2.448
10.20




G %
58.36
1.632
20.40




C %
37.95
91.83
57.95


196
transcription cofactor activity (1.23, 3.9E−4, 6.2E−1);

c
g
c



transcription cofactor activity (1.07, 3.9E−4, 6.2E−1);
A %
28.57
5.612
17.85



signal-anchor (0.99, 2.1E−3, 6.1E−1);
T %
15.30
2.551
3.571




G %
22.95
88.26
33.67




C %
33.16
3.571
44.89


177
defensin (2.34, 2.7E−4, 3.1E−1); SF001875: mammalian

t
c
c



defensin (2.34, 3.6E−4, 6.1E−1); Mammalian defensin
A %
6.214
12.42
9.039



(2.34, 4.4E−4, 5.3E−1); DEFSN (2.34, 4.5E−4, 2.3E−1);
T %
46.89
7.344
10.73



fungicide (2.34, 1.2E−3, 4.2E−1); antibiotic (2.34, 1.6E−3,
G %
33.33
4.519
3.389



4.2E−1); antimicrobial (2.34, 1.7E−3, 3.8E−1); homodimer
C %
13.55
75.70
76.83



(2.34, 2.3E−3, 4.0E−1);


175
zinc ion binding (1.72, 1.5E−5, 3.8E−2); transition metal

g
a
g



ion binding (1.72, 6.4E−5, 7.8E−2); zinc (1.72, 7.1E−4,
A %
7.428
66.85
18.85



6.2E−1); nuclear protein (1.72, 9.1E−4, 4.6E−1); zinc-
T %
6.285
9.142
16.57



finger (1.72, 1.4E−3, 4.8E−1);
G %
50.85
4
61.71




C %
35.42
20
2.857


165
membrane (1.34, 6.2E−4, 3.4E−1);

g
a
g




A %
16.96
53.33
16.96




T %
9.090
18.78
1.212




G %
41.81
18.78
78.18




C %
32.12
9.090
3.636


161
Glycoside hydrolase family 13 (2.56, 7.0E−5, 3.0E−1);

g
a
a



Alpha amylase, all-beta (2.56, 7.0E−5, 3.0E−1); Aamy_C
A %
12.42
73.91
93.78



(2.56, 9.2E−5, 5.2E−2); SF500178: alpha-amylase, short
T %
4.968
0
0.621



form (2.56, 1.2E−4, 2.6E−1); SF001019: alpha-amylase
G %
76.39
25.46
3.726



(2.56, 1.2E−4, 2.6E−1); binding site: Chloride (2.56, 3.0E−4,
C %
6.211
0.621
1.863



6.9E−1); Alpha amylase, catalytic region (2.56, 3.5E−4,



4.5E−1); Alpha amylase, catalytic subdomain (2.56, 3.5E−4,



4.5E−1); amylase activity (2.56, 4.3E−4, 6.6E−1); alpha-



amylase activity (2.56, 4.3E−4, 6.6E−1); Aamy (2.56,



4.6E−4, 1.2E−1);


106
nucleotide binding (3.76, 3.2E−5, 7.6E−2); nucleotide-

c
t
t



binding (3.76, 3.8E−5, 5.1E−2); ATP binding (3.76, 6.4E−5,
A %
16.03
2.830
5.660



7.7E−2); adenyl nucleotide binding (3.76, 9.8E−5, 7.9E−2);
T %
5.660
54.71
92.45



purine nucleotide binding (3.76, 1.5E−4, 8.8E−2); atp-
G %
29.24
0.943
0



binding (3.76, 1.5E−4, 9.8E−2);
C %
49.05
41.50
1.886


104
keratin (4.63, 2.9E−8, 4.0E−5); repeat: 6 (4.63, 5.7E−8,

g
a
c



2.3E−4); repeat: 5 (4.63, 1.5E−7, 2.9E−4); repeat: 1 (4.63,
A %
39.42
72.11
3.846



2.6E−7, 3.5E−4); repeat: 2 (4.63, 2.7E−7, 2.7E−4); repeat: 4
T %
2.884
0.961
1.923



(4.63, 3.4E−7, 2.7E−4); intermediate filament cytoskeleton
G %
41.34
6.730
43.26



(4.63, 9.3E−7, 5.8E−4); intermediate filament (4.63, 9.3E−7,
C %
16.34
20.19
50.96



5.8E−4); repeat: 3 (4.63, 1.0E−6, 6.8E−4); repeat: 7 (4.63,



9.8E−6, 5.6E−3); repeat: 8 (4.63, 1.1E−3, 4.3E−1);



SF000050: human cytochrome P450 CYP4B1 (2.01, 9.6E−6,



2.4E−2); E-class P450, group I (2.01, 5.5E−5, 2.5E−1);



electron transport (2.01, 1.2E−4, 3.3E−1); generation of



precursor metabolites and energy (2.01, 2.0E−4, 2.9E−1);



Cytochrome P450 (2.01, 2.3E−4, 4.5E−1); monooxygenase



(2.01, 3.4E−4, 2.1E−1); tetrapyrrole binding (2.01, 8.7E−4,



5.2E−1); heme binding (2.01, 8.7E−4, 5.2E−1); heme



(2.01, 1.2E−3, 4.2E−1); monooxygenase activity (2.01,



1.2E−3, 5.3E−1); SCP (1.91, 1.6E−3, 6.1E−1);


104
structural protein (1.38, 3.6E−4, 3.9E−1); cytoskeleton

a
a
g



(1.38,1.5E−3, 6.5E−1);
A %
92.30
80.76
33.65




T %
1.923
3.846
0.961




G %
1.923
12.5
60.57




C %
3.846
2.884
4.807


101
organelle envelope (2.43, 1.4E−3, 5.8E−1); envelope

c
a
a



(2.43, 1.6E−3, 3.8E−1); nuclear envelope (2.43, 7.0E−3,
A %
3.960
51.48
88.11



5.8E−1); endomembrane system (2.43, 1.3E−2, 6.8E−1);
T %
15.84
6.930
2.970



cytoplasm (1.34, 3.2E−3, 4.8E−1); intracellular (1.34,
G %
33.66
10.89
4.950



5.0E−3, 5.4E−1); electron transport (1.13, 5.3E−4, 3.0E−1);
C %
46.53
30.69
3.960



OXIDATIVE PHOSPHORYLATION (1.13, 4.9E−3,



6.2E−1);


82
transmembrane (1.68, 1.6E−3, 6.5E−1);

c
t
g




A %
1.219
0
0




T %
24.39
97.56
8.536




G %
18.29
2.439
80.48




C %
56.09
0
10.97


76
SF001638: cystatin (2.05, 1.4E−4, 3.1E−1); site: Reactive

c
g
g



site (2.05, 2.6E−4, 6.5E−1); thiol protease inhibitor (2.05,
A %
13.15
40.78
3.947



8.4E−4, 6.8E−1); CY (2.05, 1.4E−3, 5.6E−1);
T %
3.947
11.84
5.263




G %
35.52
46.05
89.47




C %
47.36
1.315
1.315


75
Keratin, high sulfur B2 protein (3.3, 5.8E−6, 3.0E−2);

c
a
c



repeat: 18 (3.3, 9.1E−6, 3.6E−2); keratin filament (3.3,
A %
0
54.66
1.333



1.1E−5, 6.5E−3); intermediate filament cytoskeleton (3.3,
T %
2.666
9.333
4



2.4E−4, 4.9E−2); intermediate filament (3.3, 2.4E−4, 4.9E−2);
G %
1.333
6.666
26.66



plasma membrane (0.85, 6.9E−3, 6.6E−1);
C %
96
29.33
68


72
tumor antigen (6.54, 9.0E−14, 1.2E−10); domain: MAGE

a
g
a



(6.54, 3.5E−11, 1.4E−7); SF005491: tumor associated
A %
68.05
0
50



protein MAGE (6.54, 3.9E−11, 1.0E−7); MAGE protein
T %
2.777
6.944
1.388



(6.54, 2.1E−10, 1.1E−6); multigene family (6.54, 3.9E−7,
G %
26.38
90.27
11.11



2.6E−4); antigen (6.54, 8.1E−6, 3.7E−3);
C %
2.777
2.777
37.5


72
nuclear protein (2.71, 3.6E−8, 4.9E−5); transcription (2.71,

g
g
a



2.7E−6, 1.8E−3); transcription regulation (2.71, 3.4E−6,
A %
44.44
1.388
47.22



1.5E−3); KRAB box (2.71, 4.4E−5, 2.0E−1); zinc finger
T %
2.777
1.388
11.11



region: C2H2-type 9 (2.71, 8.6E−5, 2.9E−1); KRAB (2.71,
G %
52.77
95.83
33.33



9.0E−5, 5.1E−2); dna-binding (2.71, 1.0E−4, 3.4E−2);
C %
0
1.388
8.333



intracellular membrane-bound organelle (2.71, 7.6E−4,



2.1E−1); metal-binding (2.71, 1.2E−3, 2.7E−1); regulation



of nucleobase, nucleoside, nucleotide and nucleic acid



metabolism (2.71, 1.3E−3, 5.8E−1);


71
SF002282: cytoskeletal keratin (1.84, 1.3E−4, 2.9E−1);

c
t
t



intermediate filament (1.84, 3.3E−4, 3.6E−1); keratin
A %
40.84
0
5.633



(1.84, 2.2E−3, 6.3E−1);
T %
0
91.54
76.05




G %
0
1.408
1.408




C %
59.15
7.042
16.90


69
KRAB box (3.66, 2.1E−10, 1.1E−6); Zinc finger, C2H2-

c
t
g



subtype (3.66, 1.4E−9, 3.6E−6); KRAB (3.66, 3.4E−9,
A %
1.449
27.53
14.49



2.0E−6); zinc (3.66, 6.7E−9, 9.1E−6); Zinc finger, C2H2-
T %
23.18
72.46
1.449



type (3.66, 8.8E−9, 1.5E−5); zinc-finger (3.66, 1.1E−8,
G %
2.898
0
76.81



7.6E−6); transcription (3.66, 7.1E−8, 3.2E−5); transcription
C %
72.46
0
7.246



regulation (3.66, 9.5E−8, 3.2E−5); zinc ion binding (3.66,



1.4E−7, 3.5E−4); transition metal ion binding (3.66, 1.5E−7,



1.8E−4); ZnF_C2H2 (3.66, 1.6E−7, 4.6E−5); metal-



binding (3.66, 2.9E−7, 7.9E−5); nuclear protein (3.66,



2.6E−6, 6.0E−4); cation binding (3.66, 3.5E−6, 2.9E−3);



zinc finger region: C2H2-type 8 (3.66, 1.1E−5, 4.2E−2);



regulation of transcription (3.66, 1.2E−5, 4.1E−2); metal



ion binding (3.66, 1.2E−5, 6.3E−3); ion binding (3.66,



1.2E−5, 6.3E−3); regulation of nucleobase, nucleoside,



nucleotide and nucleic acid metabolism (3.66, 1.5E−5,



2.5E−2); regulation of transcription, DNA-dependent



(3.66, 2.0E−5, 2.2E−2); zinc finger region: C2H2-type 7



(3.66, 2.1E−5, 4.2E−2); domain: KRAB (3.66, 2.2E−5,



2.9E−2); transcription (3.66, 2.4E−5, 2.0E−2);



transcription, DNA-dependent (3.66, 3.0E−5, 2.0E−2);



regulation of cellular metabolism (3.66, 3.4E−5, 1.9E−2);



zinc finger region: C2H2-type 6 (3.66, 3.5E−5, 3.5E−2);



General function prediction only (3.66, 4.4E−5, 3.0E−3);



regulation of metabolism (3.66, 5.0E−5, 2.4E−2); zinc



finger region: C2H2-type 5 (3.66, 8.1E−5, 6.3E−2); zinc



finger region: C2H2-type 4 (3.66, 1.3E−4, 8.6E−2); zinc



finger region: C2H2-type 1 (3.66, 1.6E−4, 8.6E−2); nucleic



acid binding (3.66, 1.9E−4, 7.5E−2); zinc finger



region: C2H2-type 2 (3.66, 2.5E−4, 1.2E−1); zinc finger



region: C2H2-type 3 (3.66, 2.9E−4, 1.2E−1); nucleobase,



nucleoside, nucleotide and nucleic acid metabolism (3.66,



5.5E−4, 2.1E−1); regulation of cellular physiological



process (3.66, 7.0E−4, 2.3E−1); regulation of



physiological process (3.66, 1.0E−3, 3.0E−1); regulation



of biological process (3.66, 1.1E−3, 3.0E−1); regulation of



cellular process (3.66, 1.3E−3, 3.1E−1); dna-binding (3.66,



4.5E−3, 5.9E−1);


67
signal (2.42, 9.0E−5, 1.2E−1); glycoprotein (2.42, 5.7E−4,

c
t
g



3.2E−1); sushi (2.17, 3.3E−3, 6.8E−1); domain: Ig-like C2-
A %
5.970
0
20.89



type 3 (1.73, 1.9E−4, 5.3E−1); cell adhesion (1.73, 5.0E−3,
T %
2.985
70.14
0



6.8E−1); transcription regulation (1.27, 1.5E−3, 4.8E−1);
G %
2.985
28.35
76.11




C %
88.05
1.492
2.985


63
GLUTATHIONE METABOLISM (1.93, 5.5E−3, 6.6E−1);

a
c
t




A %
87.30
3.174
7.936




T %
0
6.349
84.12




G %
6.349
7.936
3.174




C %
6.349
82.53
4.761


60
cellular metabolism (1.98, 1.3E−5, 4.4E−2); metabolism

c
c
c



(1.98, 7.5E−5, 1.2E−1); primary metabolism (1.98, 8.6E−4,
A %
1.666
1.666
3.333



6.2E−1); cellular physiological process (1.98, 9.7E−4,
T %
1.666
36.66
0



5.6E−1); intracellular membrane-bound organelle (1.98,
G %
0
6.666
3.333



1.9E−3, 6.9E−1); membrane-bound organelle (1.98, 1.9E−3,
C %
96.66
55
93.33



4.4E−1); regulation of cellular process (1.98, 2.4E−3,



6.9E−1); cytoplasm (1.98, 4.7E−3, 6.3E−1); intracellular



(1.98, 5.8E−3, 6.0E−1); intracellular organelle (1.98, 8.4E−3,



6.5E−1); organelle (1.98, 8.5E−3, 5.9E−1);


50
domain: KRAB (13.16, 2.7E−29, 1.1E−25); KRAB box

a
g
c



(13.16, 1.9E−27, 1.0E−23); KRAB (13.16, 1.9E−24, 1.1E−21);
A %
100
6
4



zinc finger region: C2H2-type 10 (13.16, 2.7E−24,
T %
0
10
16



5.4E−21); Zinc finger, C2H2-subtype (13.16, 3.7E−24,
G %
0
84
2



9.6E−21); zinc finger region: C2H2-type 7 (13.16, 8.0E−24,
C %
0
0
78



1.1E−20); transcription (13.16, 3.4E−19, 4.6E−16);



transcription regulation (13.16, 5.4E−19, 3.6E−16); zinc



finger region: C2H2-type 3 (13.16, 8.9E−19, 3.2E−16);



zinc finger region: C2H2-type 5 (13.16, 9.8E−19, 3.3E−16);



dna-binding (13.16, 1.3E−17, 4.6E−15); regulation of



nucleobase, nucleoside, nucleotide and nucleic acid



metabolism (13.16, 7.1E−14, 6.0E−11); regulation of



cellular metabolism (13.16, 2.7E−13, 1.5E−10); regulation



of metabolism (13.16, 5.3E−13, 2.3E−10); nucleic acid



binding (13.16, 4.8E−10, 3.0E−7); primary metabolism



(13.16, 1.6E−5, 4.2E−3); intracellular membrane-bound



organelle (13.16, 3.5E−5, 1.1E−2); zinc finger



region: C2H2-type 14 (7.98, 3.1E−16, 9.5E−14); zinc



finger region: C2H2-type 15 (7.98, 2.3E−13, 6.3E−11);



zinc finger region: C2H2-type 16 (7.98, 1.1E−8, 2.7E−6);



zinc finger region: C2H2-type 17 (7.98, 5.3E−6, 1.1E−3);



zinc finger region: C2H2-type 18 (7.98, 1.1E−4, 2.1E−2);



zinc finger region: C2H2-type 19 (7.98, 2.7E−3, 3.9E−1);



SF005559: zinc finger protein ZFP-36 (3.77, 9.7E−7, 2.5E−3);


47
B melanoma antigen (2.56, 3.3E−8, 1.7E−4);

t
g
c




A %
46.80
25.53
34.04




T %
48.93
6.382
0




G %
2.127
65.95
0




C %
2.127
2.127
65.95


45
zinc-finger (2.04, 1.0E−4, 1.3E−1); ion binding (2.04,

g
g
c



3.4E−4, 3.5E−1); metal ion binding (2.04, 3.4E−4, 3.5E−1);
A %
0
26.66
0



zinc (2.04, 5.4E−4, 3.1E−1); cation binding (2.04, 5.8E−4,
T %
0
13.33
40



3.8E−1); metal-binding (2.04, 8.0E−4, 3.0E−1); zinc ion
G %
100
48.88
2.222



binding (2.04, 8.7E−4, 4.2E−1); transition metal ion
C %
0
11.11
57.77



binding (2.04, 1.1E−3, 4.3E−1); DNA binding (2.04, 1.6E−3,



4.8E−1); DNA binding (1.33, 1.6E−3, 4.8E−1); DNA



binding (0.99, 1.6E−3, 4.8E−1);


44
DNA binding (1.99, 9.4E−4, 6.9E−1);

g
c
c




A %
0
0
4.545




T %
0
0
18.18




G %
90.90
0
2.272




C %
9.090
100
75


44
Zinc finger, C2H2-subtype (2.11, 2.9E−9, 1.5E−5);

g
a
g



ZnF_C2H2 (2.11, 1.4E−6, 8.2E−4); Zinc finger, C2H2-
A %
2.272
100
0



type (2.11, 2.5E−6, 6.4E−3); KRAB (2.11, 8.7E−6, 2.5E−3);
T %
0
0
0



zinc-finger (2.11, 1.1E−5, 1.4E−2); zinc ion binding
G %
95.45
0
97.72



(2.11, 4.3E−5, 1.0E−1); transition metal ion binding (2.11,
C %
2.272
0
2.272



5.3E−5, 6.4E−2); zinc (2.11, 6.2E−5, 4.1E−2); metal-



binding (2.11, 7.6E−5, 3.4E−2); nucleic acid binding (2.11,



4.5E−4, 3.1E−1); ion binding (2.11, 8.1E−4, 3.3E−1); metal



ion binding (2.11, 8.1E−4, 3.3E−1); cation binding (2.11,



1.5E−3, 4.7E−1); transcription (2.11, 2.5E−3, 5.7E−1);



transcription regulation (2.11, 2.8E−3, 5.3E−1); nuclear



protein (2.11, 4.7E−3, 6.6E−1); Transcription/Cell



division and chromosome partitioning (2.11, 5.9E−3,



1.8E−1);


43
domain: MAGE (3.45, 2.3E−5, 8.9E−2); MAGE protein

a
c
a



(3.45, 2.4E−5, 1.2E−1); antigen (3.45, 4.5E−4, 4.6E−1);
A %
67.44
4.651
100




T %
11.62
4.651
0




G %
0
9.302
0




C %
20.93
81.39
0













Size of Cluster




(number of
Distribution of nucleotides per position



context
along the context sequence (%)















sequences))
−6
−5
−4
−3
−2
−1







1562
g
c
c
a
c
c




5.121
6.978
4.737
65.55
3.329
1.728




4.929
7.746
2.240
2.176
6.402
0.896




72.79
33.73
8.130
29.89
10.94
3.713




17.15
51.53
84.89
2.368
79.32
93.66



987
g
g
a
g
c
c




14.89
3.850
39.31
1.722
4.863
1.013




8.510
7.700
9.827
0.607
5.065
1.013




47.01
46.80
17.62
95.84
3.444
4.964




29.58
41.64
33.23
1.823
86.62
93.00



407
a
g
c
a
c
c




75.92
3.194
1.474
92.62
7.371
3.931




12.28
2.702
0.737
0.491
5.896
0.982




7.371
92.62
24.81
5.159
19.16
7.862




4.422
1.474
72.97
1.719
67.56
87.22



398
g
c
c
a
a
g




2.512
5.778
2.763
93.96
75.87
3.015




18.34
9.547
2.010
0
0
1.005




69.59
35.17
16.83
2.010
21.10
87.68




9.547
49.49
78.39
4.020
3.015
8.291



368
c
c
c
g
c
c




3.532
1.086
27.71
1.630
2.989
2.445




10.59
12.5
2.173
0.271
2.173
1.630




16.84
6.793
20.38
96.73
1.630
4.891




69.02
79.61
49.72
1.358
93.20
91.03



347
t
c
c
a
g
g




16.71
4.034
6.628
92.21
30.54
3.746




36.59
18.73
4.034
2.017
0.864
1.440




12.39
32.85
8.357
2.593
66.85
78.67




34.29
44.38
80.97
3.170
1.729
16.13



245
g
a
g
g
c
c




8.979
35.91
0.816
10.61
1.632
8.979




4.489
6.938
1.224
2.448
0
2.857




62.04
23.26
97.95
84.08
15.10
27.34




24.48
33.87
0
2.857
83.26
60.81



196
g
g
g
a
a
g




35.71
28.06
1.530
97.44
68.87
2.040




2.040
2.040
0.510
0
0.510
1.020




57.65
67.34
97.44
2.040
30.10
94.89




4.591
2.551
0.510
0.510
0.510
2.040



177
c
c
a
g
c
c




23.72
2.824
77.40
25.42
2.824
2.259




22.59
3.389
6.779
0.564
2.259
2.259




3.954
0
11.86
74.01
2.824
1.694




49.71
93.78
3.954
0
92.09
93.78



175
g
a
g
a
a
g




4.571
68.57
8
52.57
95.42
12.57




1.714
28
2.285
0.571
1.142
1.142




74.85
1.142
85.14
44
2.857
84




18.85
2.285
4.571
2.857
0.571
2.285



165
g
g
a
g
c
c




1.818
17.57
92.12
30.90
26.06
1.212




3.636
4.848
3.636
0
0.606
1.212




92.12
44.24
3.636
67.27
21.21
3.030




2.424
33.33
0.606
1.818
52.12
94.54



161
a
g
c
a
a
a




41.61
21.73
38.50
97.51
93.78
66.45




14.90
33.54
6.211
0
1.242
1.242




16.77
39.13
13.66
1.242
1.242
29.81




26.70
5.590
41.61
1.242
3.726
2.484



106
t
c
c
a
a
a




0.943
1.886
5.660
83.96
86.79
66.03




62.26
41.50
1.886
1.886
2.830
2.830




27.35
3.773
2.830
3.773
4.716
30.18




9.433
52.83
89.62
10.37
5.660
0.943



104
a
g
a
a
c
c




98.07
3.846
69.23
88.46
3.846
18.26




1.923
5.769
2.884
1.923
8.653
8.653




0
88.46
10.57
1.923
7.692
14.42




0
1.923
17.30
7.692
79.80
58.65



104
a
a
g
a
a
a




76.92
72.11
19.23
98.07
88.46
61.53




1.923
6.730
9.615
0
1.923
3.846




1.923
17.30
61.53
1.923
0.961
14.42




19.23
3.846
9.615
0
8.653
20.19



101
g
c
c
a
a
g




24.75
3.960
0
93.06
92.07
15.84




0.990
9.900
2.970
1.980
0.990
0.990




70.29
8.910
0.990
3.960
3.960
73.26




3.960
77.22
96.03
0.990
2.970
9.900



82
g
g
g
a
a
c




7.317
4.878
20.73
80.48
54.87
40.24




3.658
3.658
6.097
13.41
0
2.439




86.58
85.36
62.19
3.658
20.73
8.536




2.439
6.097
10.97
2.439
24.39
48.78



76
g
a
g
a
c
c




1.315
89.47
3.947
61.84
17.10
1.315




3.947
6.578
2.631
1.315
26.31
2.631




90.78
3.947
93.42
30.26
26.31
14.47




3.947
0
0
6.578
30.26
81.57



75
c
g
c
a
g
c




1.333
17.33
2.666
90.66
14.66
8




5.333
22.66
0
4
4
5.333




4
34.66
2.666
1.333
60
2.666




89.33
25.33
94.66
4
21.33
84



72
g
t
c
a
t
c




16.66
2.777
0
97.22
34.72
4.166




34.72
73.61
0
0
63.88
0




48.61
16.66
9.722
2.777
1.388
0




0
6.944
90.27
0
0
95.83



72
g
g
a
a
a
a




13.88
22.22
93.05
100
88.88
56.94




2.777
1.388
0
0
1.388
0




83.33
58.33
1.388
0
4.166
37.5




0
18.05
5.555
0
5.555
5.555



71
g
g
a
a
c
c




19.71
0
49.29
91.54
1.408
0




8.450
1.408
5.633
1.408
11.26
0




71.83
67.60
4.225
7.042
1.408
0




0
30.98
40.84
0
85.91
100



69
a
a
g
a
a
a




50.72
98.55
28.98
89.85
84.05
81.15




5.797
0
0
1.449
5.797
7.246




26.08
0
66.66
4.347
2.898
10.14




17.39
1.449
4.347
4.347
7.246
1.449



67
c
c
c
a
g
c




2.985
26.86
19.40
94.02
4.477
7.462




23.88
4.477
5.970
2.985
0
2.985




31.34
0
11.94
2.985
95.52
10.44




41.79
68.65
62.68
0
0
79.10



63
g
c
a
a
t
c




1.587
20.63
82.53
74.60
4.761
1.587




0
6.349
11.11
3.174
47.61
0




98.41
12.69
0
20.63
20.63
3.174




0
60.31
6.349
1.587
26.98
95.23



60
g
c
c
g
c
g




31.66
1.666
3.333
1.666
0
3.333




5
0
1.666
3.333
0
0




63.33
33.33
0
90
5
96.66




0
65
95
5
95
0



50
c
t
a
g
a
a




8
28
68
0
96
82




0
44
0
0
0
2




8
28
30
100
4
0




84
0
2
0
0
16



47
a
g
c
a
a
g




87.23
4.255
2.127
93.61
100
0




0
4.255
25.53
0
0
2.127




8.510
87.23
2.127
4.255
0
95.74




4.255
4.255
70.21
2.127
0
2.127



45
g
g
a
g
a
c




0
22.22
93.33
2.222
95.55
0




20
4.444
2.222
0
2.222
2.222




77.77
51.11
4.444
97.77
2.222
35.55




2.222
22.22
0
0
0
62.22



44
g
c
c
c
g
g




9.090
6.818
0
2.272
0
0




2.272
0
2.272
9.090
4.545
6.818




86.36
6.818
29.54
27.27
77.27
93.18




2.272
86.36
68.18
61.36
18.18
0



44
g
c
a
g
g
g




4.545
4.545
77.27
45.45
31.81
13.63




29.54
0
4.545
0
2.272
4.545




47.72
0
18.18
50
54.54
81.81




18.18
95.45
0
4.545
11.36
0



43
g
c
c
a
g
c




0
2.325
6.976
100
30.23
2.325




2.325
2.325
2.325
0
20.93
4.651




81.39
4.651
2.325
0
32.55
0




16.27
90.69
88.37
0
16.27
93.02

















TABLE 3





Emerging gene clusters which were identified by the clustering algorithm pertaining Mus Musculus.


The below clusters are arranged according to declining size. For each cluster, the table depicts


the distribution of nucleotides for each position along the context sequence.
















Size of Cluster










(number of

Distribution of nucleotides per position


context
Function attributes set (Enrichment
along the context sequence (%)












sequences)
score/P_value/Benjamini)
Pos:
−9
−8
−7





1197
intracellular non-membrane-bound organelle (7.46, 1.0E−9,

g
c
c



1.6E−7); non-membrane-bound organelle (7.46, 1.0E−9,
A %
11.44
2.756
27.23



1.6E−7); cytoskeleton (7.46, 1.2E−9, 1.5E−7); organelle
T %
8.103
5.430
16.95



organization and biogenesis (7.46, 1.2E−3, 2.2E−1);
G %
57.14
14.70
10.02



transport (5.55, 2.2E−11, 6.4E−9); transport (5.55, 4.0E−5,
C %
23.30
77.10
45.78



2.4E−2); transporter activity (5.55, 1.1E−3, 1.2E−1); actin



cytoskeleton (4.99, 1.1E−7, 8.7E−6); actin-binding (4.99,



1.5E−6, 1.2E−4); cytoskeletal protein binding (4.99, 1.6E−4,



3.6E−2); actin binding (4.99, 3.8E−4, 6.9E−2); protein



transport (3.84, 5.5E−7, 5.3E−5); cell organization and



biogenesis (3.84, 1.1E−5, 9.6E−3); protein transporter



activity (3.84, 4.4E−5, 1.2E−2); protein localization (3.84,



1.1E−4, 5.4E−2); protein transport (3.84, 2.7E−4, 1.2E−1);



establishment of protein localization (3.84, 3.7E−4, 1.4E−1);



intracellular transport (3.84, 7.7E−4, 1.8E−1); establishment



of cellular localization (3.84, 9.0E−4, 1.9E−1); cellular



localization (3.84, 1.1E−3, 2.2E−1); intracellular protein



transport (3.84, 2.1E−3, 3.1E−1); tissue kallikrein activity



(3.41, 1.3E−12, 3.3E−9); serine protease (3.41, 6.5E−6, 4.1E−4);



serine proteinase (3.41, 9.7E−6, 5.6E−4);



SF001135: trypsin (3.41, 2.0E−5, 4.2E−2); submandibular



gland (3.41, 2.5E−5, 1.2E−3); zymogen (3.41, 3.2E−5, 1.5E−3);



protease (3.41, 2.5E−4, 8.9E−3); Peptidase S1A,



chymotrypsin (3.41, 8.3E−4, 5.7E−1); Peptidase S1 and S6,



chymotrypsin/Hap (3.41, 1.2E−3, 5.9E−1); serine-type



endopeptidase activity (3.41, 3.5E−3, 2.9E−1); serine-type



peptidase activity (3.41, 6.4E−3, 3.9E−1); Tryp_SPc (3.41,



7.0E−3, 6.4E−1); Pleckstrin-like (3.34, 4.3E−4, 4.2E−1);



metal-binding (3.32, 6.2E−7, 5.5E−5); muscle protein (2.87,



7.5E−6, 4.5E−4); contractile fiber (2.87, 2.7E−5, 1.6E−3);



myofibril (2.87, 9.5E−5, 4.5E−3); sarcomere (2.87, 2.4E−4,



9.7E−3); muscle (2.87, 3.6E−3, 7.5E−2); cellular



macromolecule metabolism (2.87, 5.1E−3, 4.7E−1); protein



metabolism (2.87, 5.4E−3, 4.8E−1); cellular protein



metabolism (2.87, 1.1E−2, 5.7E−1); golgi stack (2.82, 3.7E−5,



1.6E−3); Golgi apparatus (2.82, 7.8E−3, 1.6E−1); Golgi



stack (2.82, 1.2E−2, 2.2E−1); basolateral plasma membrane



(2.61, 8.0E−5, 4.1E−3); adherens junction (2.61, 3.3E−4,



1.2E−2); cell-substrate adherens junction (2.61, 1.4E−3,



4.5E−2); cell-matrix junction (2.61, 2.2E−3, 5.6E−2); focal



adhesion (2.61, 4.7E−3, 1.1E−1); Proteasome component



region PCI (2.48, 1.7E−4, 3.6E−1); PINT (2.48, 9.4E−4,



1.7E−1); cell projection organization and biogenesis (2.45,



5.8E−4, 1.7E−1); cell projection biogenesis (2.45, 2.5E−3,



3.3E−1); GTPase regulator activity (2.37, 2.1E−3, 2.0E−1);



small GTPase regulator activity (2.37, 4.1E−3, 3.1E−1);



enzyme regulator activity (2.37, 8.6E−3, 4.5E−1); enzyme



binding (2.33, 1.1E−3, 1.2E−1); kinase binding (2.33, 3.7E−3,



2.9E−1); magnesium (2.23, 4.8E−4, 1.6E−2); magnesium



ion binding (2.23, 1.0E−2, 4.7E−1); mRNA metabolism



(2.21, 7.0E−4, 1.8E−1); mrna processing (2.21, 7.8E−4,



2.3E−2); mRNA processing (2.21, 1.8E−3, 2.9E−1); mrna



splicing (2.21, 2.2E−3, 5.0E−2); alkali metal ion binding



(2.19, 5.4E−3, 3.5E−1); monovalent inorganic cation



transport (2.19, 5.5E−3, 4.7E−1); cation transport (2.19,



7.9E−3, 5.3E−1); ion transport (2.19, 8.3E−3, 5.4E−1);



potassium transport (2.19, 1.2E−2, 1.7E−1); ionic channel



(2.19, 2.9E−2, 3.2E−1); Arf GTPase activating protein (2.14,



9.4E−5, 3.8E−1); ArfGap (2.14, 1.2E−4, 6.9E−2);



carbohydrate metabolism (2.09, 5.6E−4, 1.8E−2); glycogen



metabolism (2.09, 1.8E−3, 4.5E−2); glucan metabolism



(2.09, 1.4E−2, 6.3E−1); glycogen metabolism (2.09, 1.4E−2,



6.3E−1); desmosome (1.75, 3.1E−5, 1.7E−3); cell junction



(1.75, 2.2E−4, 9.6E−3); intercellular junction (1.75, 1.6E−3,



4.7E−2); apicolateral plasma membrane (1.75, 1.9E−3, 5.2E−2);



apical junction complex (1.75, 1.9E−3, 5.2E−2); sh3



domain (1.72, 2.1E−3, 5.0E−2);


710
signal (3.82, 2.4E−8, 9.0E−6); glycoprotein (3.82, 6.0E−7,

c
c
c



1.7E−4); extracellular region (3.82, 1.8E−6, 1.1E−3);
A %
6.901
8.309
4.084



extracellular space (3.82, 1.9E−6, 5.9E−4); protein
T %
9.295
17.60
2.816



metabolism (3.82, 2.1E−4, 1.4E−1; serine/threonine-protein
G %
41.69
30.56
40



kinase (2.4, 1.2E−5, 1.7E−3); transferase (2.4, 1.7E−5, 1.8E−3);
C %
42.11
43.52
53.09



atp-binding (2.4, 7.7E−5, 6.7E−3); kinase (2.4, 2.6E−4,



1.7E−2); protein serine/threonine kinase activity (2.4, 6.6E−4,



2.7E−1); protein-tyrosine kinase activity (2.4, 1.0E−3,



3.4E−1); protein amino acid phosphorylation (2.4, 1.3E−3,



3.0E−1); S_TKc (2.4, 2.0E−3, 6.9E−1); protein kinase



activity (2.4, 2.2E−3, 4.4E−1); phosphorylation (2.4, 3.7E−3,



5.1E−1); cAMP-dependent protein kinase activity (2.4,



4.2E−3, 5.4E−1); cyclic nucleotide-dependent protein kinase



activity (2.4, 4.2E−3, 5.4E−1); protein kinase CK2 activity



(2.4, 4.4E−3, 5.4E−1); phosphotransferase activity, alcohol



group as acceptor (2.4, 5.6E−3, 6.0E−1); ATP (2.4, 1.3E−2,



2.8E−1); serine/threonine-specific protein kinase (2.4, 5.6E−2,



6.3E−1); phosphotransferase (2.4, 5.9E−2, 6.3E−1);



negative regulation of biological process (2.38, 9.3E−4,



2.5E−1); negative regulation of cellular process (2.38, 1.6E−3,



3.3E−1); negative regulation of physiological process



(2.38, 1.7E−3, 3.4E−1); negative regulation of cellular



physiological process (2.38, 3.2E−3, 4.7E−1); extrinsic to



plasma membrane (2.25, 1.2E−3, 1.7E−1); extrinsic to



membrane (2.25, 1.7E−3, 1.9E−1); protein transport (2.22,



4.6E−5, 4.4E−3); cell organization and biogenesis (2.22,



9.0E−5, 1.0E−1); protein localization (2.22, 6.1E−3, 6.7E−1);



metal-binding (2.11, 4.4E−6, 8.4E−4); cell cycle (1.85, 6.5E−3,



2.0E−1); anti-oncogene (1.85, 1.6E−2, 3.2E−1); electron



transfer (1.77, 3.3E−4, 2.0E−2); chromoprotein (1.77, 5.8E−4,



3.1E−2); heme (1.77, 1.4E−3, 5.8E−2); heme binding



(1.77, 2.6E−3, 4.3E−1); tetrapyrrole binding (1.77, 2.6E−3,



4.3E−1); metalloprotein (1.77, 3.2E−3, 1.2E−1); unspecific



monooxygenase activity (1.77, 6.7E−3, 6.2E−1); iron (1.77,



7.4E−3, 2.1E−1); monooxygenase (1.77, 1.2E−2, 2.8E−1);



oxidoreductase (1.77, 1.9E−2, 3.4E−1); microsome (1.77,



4.1E−2, 5.5E−1); golgi stack (1.69, 2.1E−3, 8.1E−2);



transport (1.64, 7.3E−4, 3.7E−2);


397
metal-binding (3.5, 6.9E−6, 2.6E−3); zinc (3.5, 5.6E−5, 1.1E−2);

c
g
g



cation binding (3.5, 1.8E−4, 1.3E−1); ion binding (3.5,
A %
21.41
18.63
5.541



3.2E−4, 1.8E−1); metal ion binding (3.5, 3.2E−4, 1.8E−1);
T %
13.09
13.85
5.793



transition metal ion binding (3.5, 9.0E−4, 3.0E−1); zinc ion
G %
29.97
48.61
61.96



binding (3.5, 3.2E−3, 6.3E−1); zinc-finger (3.5, 5.0E−3,
C %
35.51
18.89
26.70



3.3E−1); nuclear protein (3.19, 1.5E−8, 1.7E−5); organelle



(3.19, 2.8E−4, 1.6E−1); intracellular organelle (3.19, 6.5E−4,



1.8E−1); membrane-bound organelle (3.19, 1.1E−3, 2.1E−1);



intracellular membrane-bound organelle (3.19, 2.4E−3,



3.1E−1); nucleus (3.19, 3.3E−3, 3.4E−1); intracellular (3.19,



5.4E−3, 4.3E−1); nuclear protein (2.99, 1.5E−8, 1.7E−5);



regulation of metabolism (2.99, 9.4E−5, 8.2E−2);



transcription (2.99, 1.7E−4, 2.4E−2); regulation of



physiological process (2.99, 2.1E−4, 1.0E−1); regulation of



biological process (2.99, 2.2E−4, 9.5E−2); ); transcription,



DNA-dependent (2.99, 1.0E−3, 2.1E−1);;



metalloexopeptidase activity (1.22, 2.1E−3, 5.2E−1);



glycosyltransferase (1.09, 2.1E−2, 6.9E−1); calcium (1.09,



1.4E−2, 5.6E−1); transport (0.96, 1.3E−2, 5.4E−1);



nucleotide-binding (0.43, 2.2E−2, 6.9E−1);


357
ribosomal protein (4.97, 2.6E−8, 3.0E−5); ribonucleoprotein

g
c
g



(4.97, 3.8E−8, 2.2E−5); macromolecule biosynthesis (4.97,
A %
5.602
18.76
23.80



4.6E−7, 8.3E−4); cellular biosynthesis (4.97, 5.9E−7, 7.2E−4);
T %
4.761
5.602
6.162



biosynthesis (4.97, 7.1E−7, 6.4E−4); structural
G %
71.70
29.69
35.57



constituent of ribosome (4.97, 2.3E−6, 5.5E−3); ribosome
C %
17.92
45.93
34.45



(4.97, 4.5E−6, 9.2E−4); RIBOSOME (4.97, 5.8E−6, 1.1E−3);



protein biosynthesis (4.97, 1.6E−5, 1.1E−2);



ribonucleoprotein complex (4.97, 6.6E−5, 1.0E−2);



structural molecule activity (4.97, 9.4E−4, 4.3E−1); transport



(3.53, 1.1E−4, 2.5E−2); transporter activity (3.53, 1.2E−4,



1.3E−1); establishment of localization (3.53, 5.0E−4, 2.3E−1);



transport (3.53, 5.7E−4, 2.0E−1); localization (3.53,



6.4E−4, 2.1E−1);


373
cytoplasm (2.19, 6.6E−5, 4.0E−2); intracellular (2.19, 1.2E−3,

g
g
c



3.1E−1); intracellular organelle (2.19, 4.3E−3, 4.8E−1);
A %
13.13
7.774
2.680



organelle (2.19, 4.6E−3, 4.3E−1); Defensin propeptide (2.16,
T %
6.702
21.17
2.949



1.1E−4, 4.3E−1); membrane (2.04, 5.8E−9, 6.6E−6);
G %
49.06
58.98
9.383



glycoprotein (2.04, 2.0E−5, 1.1E−2); transmembrane (2.04,
C %
31.09
12.06
84.98



5.2E−5, 2.0E−2); signal (2.04, 1.8E−3, 2.0E−1); extracellular



region (2.04, 6.0E−3, 4.1E−1); extracellular space (2.04,



8.8E−3, 4.9E−1); ribosomal protein (1.99, 6.8E−5, 1.9E−2);



structural constituent of ribosome (1.99, 7.5E−4, 6.0E−1);



ribonucleoprotein (1.99, 1.3E−3, 1.7E−1); ribosome (1.99,



5.0E−3, 4.0E−1); heparin binding (1.94, 1.8E−3, 6.6E−1);



heparin-binding (1.94, 1.2E−2, 5.0E−1); sh3 domain (1.93,



1.8E−3, 1.9E−1); transit peptide (1.69, 2.2E−3, 1.9E−1);



mitochondrion (1.69, 3.6E−3, 5.2E−1); mitochondrion (1.69,



4.8E−3, 3.2E−1); organelle inner membrane (1.69, 1.4E−2,



6.3E−1); gtp-binding (1.64, 6.1E−4, 9.5E−2); nucleotide-



binding (1.35, 4.4E−3, 3.2E−1); transport (1.32, 2.2E−3,



2.0E−1); heat shock (1.03, 1.9E−2, 6.4E−1); zinc (1.01, 8.8E−3,



4.5E−1); metal-binding (1.01, 1.1E−2, 5.0E−1); ubl



conjugation pathway (0.64, 1.1E−2, 4.8E−1); nuclear protein



(0.29, 2.2E−2, 6.9E−1);


290
cytolysis (3.78, 1.5E−7, 1.7E−4); SF001135: trypsin (3.78,

g
c
t



4.3E−7, 9.3E−4); serine proteinase (3.78, 1.0E−6, 5.9E−4);
A %
8.965
2.068
25.17



serine protease (3.78, 1.8E−6, 6.7E−4); cytolysis (3.78,
T %
6.551
2.068
38.27



4.5E−6, 1.6E−2); protease (3.78, 1.3E−5, 3.6E−3); zymogen
G %
61.72
32.41
11.37



(3.78, 3.4E−5, 7.6E−3); Peptidase S1A, chymotrypsin (3.78,
C %
22.75
63.44
25.17



7.1E−5, 8.7E−2); Tryp_SPc (3.78, 9.7E−5, 2.8E−2);



domain: Peptidase S1 (3.78, 1.1E−4, 2.9E−1); serine-type



endopeptidase activity (3.78, 1.5E−4, 3.0E−1); Peptidase S1



and S6, chymotrypsin/Hap (3.78, 1.8E−4, 1.4E−1); serine-



type peptidase activity (3.78, 2.3E−4, 2.5E−1); proteolysis



(3.78, 1.7E−3, 4.9E−1); t-cell (3.78, 2.1E−3, 1.7E−1);



peptidase activity (3.78, 2.4E−3, 6.9E−1); hydrolase (3.78,



2.5E−3, 1.7E−1); direct protein sequencing (3.78, 4.6E−3,



2.5E−1); SF001714: Bcl2 related apoptosis regulator (3.2,



3.1E−6, 3.4E−3); Bcl2 related apoptosis regulator (3.2, 4.4E−6,



2.3E−2); Apoptosis regulator, Bcl-2 related (3.2, 7.3E−6,



1.9E−2); BCL (3.2, 1.9E−5, 1.1E−2); BCL2-like apoptosis



inhibitor (3.2, 2.7E−5, 4.6E−2); Apoptosis regulator Bcl-2,



BH (3.2, 1.1E−4, 1.1E−1); cell death (3.2, 3.2E−4, 1.5E−1);



death (3.2, 3.8E−4, 1.6E−1); cellular physiological process



(2.27, 1.6E−5, 2.9E−2); protein metabolism (2.27, 7.7E−5,



8.9E−2); cellular macromolecule metabolism (2.27, 7.9E−5,



6.9E−2); cellular protein metabolism (2.27, 1.1E−4, 7.4E−2);



macromolecule metabolism (2.27, 2.4E−4, 1.4E−1); nuclear



protein (1.62, 4.1E−3, 2.4E−1); signal (1.61, 7.7E−5, 1.2E−2);



glycoprotein (1.61, 3.7E−4, 4.6E−2); metal-binding



(1.41, 1.4E−3, 1.2E−1); zinc (1.41, 2.2E−3, 1.6E−1); zinc-



finger (1.41, 1.2E−2, 4.0E−1); nuclear pore (1.38, 9.6E−3,



6.9E−1); pore complex (1.38, 9.6E−3, 6.9E−1); chaperone



(1.17, 2.3E−2, 6.0E−1); cell cycle (1.06, 1.2E−2, 4.0E−1);



nucleotide-binding (1.02, 6.5E−3, 3.1E−1); transferase (1.02,



7.7E−3, 3.4E−1); atp-binding (1.02, 2.0E−2, 5.7E−1);



membrane (0.95, 7.8E−4, 7.8E−2); transmembrane (0.95,



1.0E−2, 3.8E−1); glycosyltransferase (0.92, 5.7E−3, 2.9E−1);



rna-binding (0.92, 7.9E−3, 3.4E−1); glycosyltransferase



(0.91, 5.7E−3, 2.9E−1); ligase (0.84, 3.0E−3, 2.0E−1);


283
Serpin B9 and maspin (3.42, 3.1E−8, 1.6E−4); protease

t
c
c



inhibitor activity (3.42, 3.0E−4, 5.1E−1); Proteinase
A %
20.84
26.50
6.713



inhibitor I4, serpin (3.42, 3.2E−4, 5.7E−1); enzyme inhibitor
T %
37.80
30.03
17.66



activity (3.42, 6.4E−4, 4.0E−1); SERPIN (3.42, 7.0E−4,
G %
20.49
12.72
30.38



1.8E−1); endopeptidase inhibitor activity (3.42, 1.4E−3,
C %
20.84
30.74
45.22



5.8E−1); transport (2.84, 7.3E−5, 2.1E−2); transporter



activity (2.84, 4.7E−4, 4.3E−1); membrane (2.77, 1.2E−9,



1.4E−6); transmembrane (2.77, 4.6E−6, 2.6E−3); oxygen



carrier (1.69, 1.3E−3, 2.2E−1); oxygen transport (1.69, 1.6E−3,



2.3E−1); oxygen transporter activity (1.69, 3.2E−3, 6.7E−1);



ribosomal protein (1.67, 8.7E−4, 1.8E−1); structural



constituent of ribosome (1.67, 4.8E−3, 6.9E−1); ribosome



(1.67, 5.3E−3, 6.6E−1); ribonucleoprotein (1.67, 1.0E−2,



6.0E−1); cytokine (1.07, 2.4E−3, 2.9E−1); glycoprotein



(0.92, 2.9E−3, 3.1E−1); signal (0.92, 3.8E−3, 3.5E−1);



cytokine (0.74, 2.4E−3, 2.9E−1); protease (0.66, 8.0E−3,



5.3E−1);


220
protein transport (2.99, 3.7E−5, 1.4E−2); golgi stack (2.99,

g
g
c



3.0E−4, 6.7E−2); Golgi stack (2.99, 2.9E−3, 2.2E−1);
A %
6.363
3.181
5.909



transport (2.99, 3.8E−3, 3.2E−1); Golgi apparatus (2.99,
T %
2.727
0.454
3.636



9.0E−3, 5.0E−1); cellular physiological process (2.46, 4.8E−6,
G %
81.36
67.72
8.636



1.7E−2); nuclear protein (2.46, 2.4E−5, 2.7E−2);
C %
9.545
28.63
81.81



intracellular (2.46, 5.7E−5, 3.5E−2); intracellular organelle



(2.46, 3.7E−4, 1.1E−1); organelle (2.46, 3.9E−4, 7.7E−2);



intracellular membrane-bound organelle (2.46, 1.6E−3,



2.2E−1); membrane-bound organelle (2.46, 1.7E−3, 1.6E−1);



mrna processing (2.07, 3.3E−4, 6.1E−2); mrna splicing



(2.07, 5.4E−3, 3.8E−1); nuclear protein (1.45, 2.4E−5, 2.7E−2);



dna-binding (1.45, 5.4E−4, 7.4E−2); transcription (1.45,



2.0E−2, 6.7E−1); protein transport (1.44, 3.7E−5, 1.4E−2);



transport (1.44, 3.8E−3, 3.2E−1); lipoprotein (1.42, 4.6E−4,



7.2E−2); gtp-binding (1.42, 5.5E−3, 3.6E−1); transit peptide



(1.34, 3.1E−3, 3.2E−1); cell cycle (1.25, 9.0E−3, 4.8E−1);



transcription (1.13, 2.0E−2, 6.7E−1); endoplasmic reticulum



(0.97, 1.9E−2, 6.7E−1); gtp-binding (0.91, 5.5E−3, 3.6E−1);



nucleotide-binding (0.91, 2.2E−2, 6.8E−1); ubl conjugation



pathway (0.76, 7.1E−3, 4.2E−1); membrane (0.32, 3.5E−3,



3.3E−1);


127
membrane (1.49, 4.0E−4, 2.0E−1); transmembrane (1.49,

g
c
c



5.1E−4, 1.8E−1); nuclear protein (0.83, 8.3E−5, 9.0E−2);
A %
7.086
3.937
1.574




T %
18.11
3.937
26.77




G %
49.60
18.89
32.28




C %
25.19
73.22
39.37


120
monooxygenase activity (1.71, 2.4E−4, 2.6E−1);

a
g
c



monooxygenase (1.71, 8.4E−4, 6.2E−1);
A %
91.66
0
13.33




T %
3.333
2.5
21.66




G %
0.833
97.5
31.66




C %
4.166
0
33.33


119
embryonic morphogenesis (1.41, 5.3E−5, 1.7E−1);

g
c
g




A %
0.840
1.680
21.84




T %
5.042
0.840
1.680




G %
79.83
1.680
75.63




C %
14.28
95.79
0.840


118
glycoprotein (1.29, 6.3E−4, 5.2E−1); membrane (1.29, 7.1E−4,

g
g
c



3.3E−1);
A %
23.72
31.35
6.779




T %
26.27
20.33
16.10




G %
44.91
47.45
24.57




C %
5.084
0.847
52.54


118
Vomeronasal receptor, type 2 (2.64, 1.7E−7, 8.9E−4);

g
c
t



metabotropic glutamate receptor signaling pathway (2.64,
A %
5.932
4.237
15.25



3.3E−7, 1.2E−3); glutamate signaling pathway (2.64, 6.3E−7,
T %
28.81
20.33
63.55



1.1E−3); metabotropic glutamate, GABA-B-like receptor
G %
33.89
25.42
7.627



activity (2.64, 2.9E−6, 6.9E−3); Extracellular ligand-binding
C %
31.35
50
13.55



receptor (2.64, 4.6E−6, 1.2E−2); glutamate receptor activity



(2.64, 1.4E−5, 1.6E−2); GPCR, family 3, metabotropic



glutamate receptor-like (2.64, 5.6E−5, 9.1E−2); cytoskeletal



protein binding (1.66, 7.8E−4, 4.7E−1);


113
glycosidase (2.36, 1.0E−3, 4.5E−1); developmental protein

g
c
c



(0.91, 2.1E−3, 3.9E−1); membrane (0.89, 1.5E−3, 3.5E−1);
A %
3.539
10.61
4.424




T %
0.884
0.884
16.81




G %
95.57
7.964
17.69




C %
0
80.53
61.06


111
natural killer cell lectin-like receptor binding (2.6, 1.6E−6,

g
a
a



3.8E−3); anchored to plasma membrane (2.6, 1.0E−5, 6.4E−3);
A %
1.801
93.69
100



anchored to membrane (2.6, 1.0E−5, 6.4E−3); lipoprotein
T %
7.207
0
0



(2.6, 2.5E−4, 2.5E−1); NATURAL KILLER CELL
G %
71.17
0
0



MEDIATED CYTOTOXICITY (2.6, 1.0E−3, 1.8E−1);
C %
19.81
6.306
0



membrane (0.65, 1.5E−3, 5.8E−1);


108
signal (0.95, 3.5E−3, 6.4E−1); dna-binding (0.68, 9.7E−4,

c
c
t



6.7E−1); nuclear protein (0.68, 1.7E−3, 6.3E−1);
A %
6.481
11.11
1.851




T %
12.96
5.555
94.44




G %
29.62
2.777
0.925




C %
50.92
80.55
2.777


95
transmembrane (1.46, 7.0E−5, 7.7E−2); membrane (1.46,

g
c
g



1.9E−4, 1.0E−1); glycoprotein (1.46, 2.9E−3, 5.6E−1);
A %
5.263
24.21
8.421



developmental protein (1.2, 1.5E−3, 4.3E−1); developmental
T %
5.263
5.263
22.10



protein (0.99, 1.5E−3, 4.3E−1); glycoprotein (0.62, 2.9E−3,
G %
87.36
4.210
36.84



5.6E−1);
C %
2.105
66.31
32.63


94
cellular physiological process (2.39, 2.6E−6, 9.3E−3);

c
t
g




A %
3.191
3.191
1.063




T %
3.191
87.23
6.382




G %
3.191
2.127
89.36




C %
90.42
7.446
3.191


86
Carboxylesterase, type B (1.63, 7.1E−5, 3.1E−1); serine

c
c
t



esterase (1.63, 1.0E−4, 1.1E−1);
A %
1.162
23.25
4.651




T %
3.488
5.813
58.13




G %
0
0
0




C %
95.34
70.93
37.20


83
Keratin, high sulfur B2 protein (2.49, 1.6E−5, 7.9E−2);

t
c
t



keratin filament (2.49, 3.4E−5, 2.1E−2);
A %
9.638
1.204
7.228




T %
87.95
4.819
86.74




G %
0
0
4.819




C %
2.409
93.97
1.204


80
glycoprotein (1.16, 1.1E−4, 1.2E−1); signal (1.16, 8.4E−4,

c
g
c



3.8E−1);
A %
1.25
3.75
10




T %
1.25
6.25
0




G %
12.5
86.25
12.5




C %
85
3.75
77.5


79
zymogen (1.33, 4.6E−4, 4.1E−1);

c
a
g




A %
36.70
96.20
21.51




T %
16.45
1.265
10.12




G %
5.063
2.531
51.89




C %
41.77
0
16.45


79
extracellular region (1.18, 6.1E−4, 3.1E−1); extracellular

g
g
a



space (1.18, 1.3E−3, 3.2E−1);
A %
1.265
5.063
94.93




T %
26.58
1.265
3.797




G %
69.62
93.67
1.265




C %
2.531
0
0


70
transmembrane (0.82, 1.6E−3, 6.0E−1);

g
c
c




A %
10
10
5.714




T %
18.57
0
15.71




G %
42.85
2.857
2.857




C %
28.57
87.14
75.71


68
membrane (1.58, 1.1E−4, 1.1E−1); glycoprotein (1.5, 1.1E−3,

a
a
a



4.8E−1); signal (1.5, 1.2E−3, 3.6E−1);
A %
85.29
54.41
91.17




T %
7.352
0
2.941




G %
1.470
29.41
4.411




C %
5.882
16.17
1.470


67
FBOX (1.74, 2.8E−9, 1.6E−6); Cyclin-like F-box (1.74,

c
c
a



1.5E−7, 7.7E−4); ubl conjugation pathway (1.74, 2.2E−3,
A %
25.37
2.985
94.02



5.7E−1); glycoprotein (1.52, 6.6E−4, 5.3E−1); signal (1.52,
T %
13.43
7.462
2.985



1.9E−3, 6.6E−1); glycoprotein (0.95, 6.6E−4, 5.3E−1);
G %
26.86
0
2.985




C %
34.32
89.55
0


64
hydrolase (1.95, 1.6E−4, 1.6E−1);

c
a
g




A %
20.31
73.43
6.25




T %
1.562
14.06
3.125




G %
9.375
9.375
48.43




C %
68.75
3.125
42.18


62
SCY (1.28, 1.9E−3, 6.8E−1); transferase (0.95, 1.7E−4, 1.7E−1);

a
c
c



.
A %
69.35
25.80
4.838




T %
3.225
20.96
3.225




G %
11.29
1.612
24.19




C %
16.12
51.61
67.74


61
transport (1.77, 4.7E−4, 2.4E−1); membrane (0.98, 1.8E−4,

c
g
g



1.9E−1);
A %
18.03
31.14
11.47




T %
8.196
0
16.39




G %
6.557
49.18
70.49




C %
67.21
19.67
1.639


61
Hormone (4.77, 4.2E−13, 4.8E−10); Somatotropin hormone

ag
c
c



(4.77, 7.6E−12, 3.9E−8); Cytokine, four-helical bundle
A %
34.42
3.278
0



(4.77, 1.7E−10, 4.3E−7); hormone activity (4.77, 2.4E−8,
T %
22.95
1.639
6.557



5.8E−5); receptor binding (4.77, 1.2E−5, 9.5E−3);
G %
34.42
4.918
0



Glycoprotein (4.77, 1.2E−5, 7.0E−3); Signal (4.77, 3.9E−5,
C %
8.196
90.16
93.44



1.5E−2); extracellular space (4.77, 5.2E−4, 2.7E−1);



extracellular region (4.77, 1.8E−3, 4.2E−1);


55
nucleotide-binding (1.94, 1.2E−4, 1.3E−1); adenyl

c
t
c



nucleotide binding (1.94, 1.6E−4, 3.1E−1); protein amino
A %
3.636
1.818
9.090



acid phosphorylation (1.94, 1.6E−4, 4.4E−1); purine
T %
25.45
87.27
16.36



nucleotide binding (1.94, 2.3E−4, 2.5E−1); phosphorylation
G %
16.36
10.90
0



(1.94, 4.0E−4, 5.2E−1); atp-binding (1.94, 5.4E−4, 2.6E−1);
C %
54.54
0
74.54



ATP binding (1.94, 5.5E−4, 2.8E−1); nucleotide binding



(1.94, 7.6E−4, 3.1E−1); phosphorus metabolism (1.94, 1.2E−3,



6.5E−1); phosphate metabolism (1.94, 1.2E−3, 6.5E−1);



kinase activity (1.94, 1.3E−3, 4.2E−1); transferase activity,



transferring phosphorus-containing groups (1.94, 3.1E−3,



6.1E−1); kinase (1.94, 3.6E−3, 6.5E−1); receptor binding



(1.84, 4.3E−4, 2.9E−1); transmembrane protein (0.53, 2.0E−3,



5.2E−1);


52
E-class P450, CYP3A (2.21, 4.0E−7, 2.1E−3);

g
a
a



METABOLISM OF XENOBIOTICS BY CYTOCHROME
A %
11.53
78.84
59.61



P450 (2.21, 2.1E−5, 4.1E−3); GAMMA-
T %
1.923
3.846
5.769



HEXACHLOROCYCLOHEXANE DEGRADATION
G %
51.92
5.769
30.76



(2.21, 2.2E−5, 2.2E−3); LINOLEIC ACID METABOLISM
C %
34.61
11.53
3.846



(2.21, 1.9E−4, 1.2E−2);


50
KRAB box (1.94, 1.3E−6, 6.6E−3); nuclear protein (1.94,

t
t
c



3.6E−5, 4.0E−2); ZnF_C2H2 (1.94, 4.4E−5, 2.5E−2); Zinc
A %
30
0
4



finger, C2H2-type (1.94, 5.3E−5, 1.3E−1); zinc-finger (1.94,
T %
44
94
4



6.3E−5, 3.5E−2); KRAB (1.94, 8.0E−5, 2.3E−2); zinc (1.94,
G %
8
6
2



3.1E−4, 1.1E−1); metal-binding (1.94, 3.4E−4, 9.4E−2);
C %
18
0
90



General function prediction only (1.94, 1.7E−2, 6.9E−1);



hyalurononglucosaminidase activity (1.8, 7.9E−5, 1.7E−1);



Glycoside hydrolase, family 56 (1.8, 8.0E−5, 1.3E−1);



hexosaminidase activity (1.8, 3.9E−4, 3.8E−1);


46
intracellular membrane-bound organelle (2.38, 4.2E−4,

c
c
t



2.3E−1); membrane-bound organelle (2.38, 4.3E−4, 1.2E−1);
A %
10.86
4.347
6.521



intracellular organelle (2.38, 2.3E−3, 3.8E−1); organelle
T %
0
4.347
84.78



(2.38, 2.4E−3, 3.1E−1); intracellular (2.38, 4.7E−3, 4.4E−1);
G %
0
8.695
4.347



nucleus (2.38, 6.1E−3, 4.6E−1); dna-binding (0.93, 9.5E−4,
C %
89.13
82.60
4.347



6.6E−1); nucleus (0.93, 6.1E−3, 4.6E−1);


42
integrin complex (1.32, 1.6E−3, 6.3E−1);

a
c
t




A %
100
7.142
4.761




T %
0
16.66
95.23




G %
0
11.90
0




C %
0
64.28
0


42
Tryp_SPc (2.24, 3.0E−4, 1.6E−1); serine protease (2.24,

g
c
t



1.0E−3, 6.9E−1);
A %
9.523
2.380
26.19




T %
23.80
9.523
73.80




G %
38.09
0
0




C %
28.57
88.09
0


41
defense response to bacteria (3.53, 5.5E−8, 2.0E−4); Beta

g
c
t



defensin (3.53, 7.7E−8, 4.0E−4); response to bacteria (3.53,
A %
2.439
0
4.878



1.4E−7, 2.4E−4); defensin (3.53, 3.4E−7, 3.9E−4); antibiotic
T %
31.70
4.878
92.68



(3.53, 4.7E−7, 2.7E−4); antimicrobial (3.53, 7.3E−7, 2.8E−4);
G %
60.97
14.63
2.439



response to stress (3.53, 5.0E−4, 4.6E−1);
C %
4.878
80.48
0


41
transmembrane (1.47, 5.4E−4, 4.6E−1); membrane (1.47,

g
a
c



2.2E−3, 5.7E−1); glycoprotein (1.19, 6.8E−4, 3.2E−1);
A %
0
60.97
2.439



plasma (1.19, 4.0E−3, 6.8E−1);
T %
12.19
4.878
2.439




G %
82.92
34.14
2.439




C %
4.878
0
92.68


40
UDP-glucuronosyl/UDP-glucosyltransferase (2.59, 3.5E−6,

a
t
t



1.8E−2); SF005678: glucuronosyltransferase (2.59, 3.7E−6,
A %
57.5
0
17.5



8.0E−3);
T %
12.5
67.5
82.5




G %
7.5
2.5
0




C %
22.5
30
0


38
SF005558: natural killer cell receptor P1 (4.28, 2.1E−12,

a
c
t



4.4E−9); lectin (4.28, 1.0E−11, 1.2E−8); C-type lectin (4.28,
A %
86.84
2.631
0



1.2E−10, 6.1E−7); CLECT (4.28, 1.3E−10, 7.4E−8); sugar
T %
2.631
0
97.36



binding (4.28, 2.2E−9, 5.4E−6); t-cell (4.28, 8.0E−9, 4.6E−6);
G %
10.52
28.94
0



carbohydrate binding (4.28, 3.0E−8, 3.6E−5); domain: C-type
C %
0
68.42
2.631



lectin (4.28, 3.5E−8, 1.1E−4); antigen (4.28, 8.9E−8, 3.4E−5);



signal-anchor (4.28, 5.5E−7, 1.6E−4); cell adhesion (4.28,



1.6E−5, 3.7E−3); receptor (4.28, 2.9E−5, 5.5E−3);



glycoprotein (4.28, 4.1E−4, 6.4E−2); multigene family (4.28,



7.1E−4, 9.6E−2); membrane (4.28, 1.5E−3, 1.7E−1);



transmembrane (4.28, 6.5E−3, 5.2E−1);













Size of Cluster




(number of
Distribution of nucleotides per position



context
along the context sequence (%)















sequences)
−6
−5
−4
−3
−2
−1







1197
g
c
c
g
c
c




4.594
9.857
36.42
47.11
2.840
1.169




6.182
8.020
5.680
0.835
3.675
1.587




81.03
25.48
6.683
50.04
2.088
4.010




8.187
56.64
51.21
2.005
91.39
93.23



710
c
g
c
g
c
c




25.91
3.521
7.183
36.61
3.802
0.845




17.04
22.39
7.887
1.408
3.661
0.422




15.91
45.77
15.91
58.87
8.450
1.549




41.12
28.30
69.01
3.098
84.08
97.18



397
a
g
g
a
a
g




44.33
25.94
8.816
96.22
89.42
5.541




13.85
9.571
8.060
0
0.251
1.511




37.27
59.94
64.23
1.763
8.060
89.16




4.534
4.534
18.89
2.015
2.267
3.778



357
g
c
c
a
g
g




5.322
3.081
1.960
88.51
40.61
3.361




5.882
18.76
1.120
1.400
3.081
2.801




63.30
3.361
3.641
5.882
52.10
70.86




25.49
74.78
93.27
4.201
4.201
22.96



373
c
c
a
g
c
c




22.25
6.702
52.54
1.340
6.970
0.536




22.52
2.412
10.72
0.536
9.115
3.485




20.64
36.19
24.39
96.51
3.217
2.680




34.58
54.69
12.33
1.608
80.69
93.29



290
g
g
g
a
a
g




3.448
26.55
7.241
75.51
82.75
11.72




0.689
12.06
2.068
1.034
3.103
1.034




93.44
47.58
80.68
22.41
11.03
83.79




2.413
13.79
10
1.034
3.103
3.448



283
t
c
c
a
c
c




18.37
7.067
5.653
96.11
4.240
1.413




49.82
4.240
2.120
0.353
35.68
1.766




20.14
10.60
3.886
2.473
13.78
1.766




11.66
78.09
88.33
1.060
46.28
95.05



220
g
g
c
g
g
g




7.727
4.090
0.454
21.81
15.45
3.181




7.272
4.545
0.909
0.909
4.090
1.818




77.27
90.45
3.181
75.90
49.54
50.90




7.727
0.909
95.45
1.363
30.90
44.09



127
g
g
g
g
c
c




2.362
18.11
0.787
2.362
2.362
0.787




18.11
8.661
6.299
0.787
0
3.149




77.16
65.35
90.55
92.91
0.787
1.574




2.362
7.874
2.362
3.937
96.85
94.48



120
c
t
c
a
c
c




6.666
15
9.166
45.83
2.5
6.666




25
75
20
3.333
4.166
3.333




22.5
2.5
20
43.33
8.333
4.166




45.83
7.5
50.83
7.5
85
85.83



119
g
c
g
g
c
c




0.840
27.73
2.521
3.361
15.12
5.882




0.840
1.680
4.201
0
4.201
5.042




92.43
5.042
56.30
88.23
11.76
35.29




5.882
65.54
36.97
8.403
68.90
53.78



118
a
g
c
a
g
g




44.91
11.86
4.237
90.67
0.847
11.86




33.89
22.03
0
3.389
0
7.627




0.847
55.93
0.847
0.847
95.76
78.81




20.33
10.16
94.91
5.084
3.389
1.694



118
g
c
a
g
a
c




0.847
8.474
85.59
1.694
83.89
22.88




0.847
5.932
11.01
0
5.084
0.847




90.67
0
0.847
96.61
4.237
10.16




7.627
85.59
2.542
1.694
6.779
66.10



113
g
g
c
a
g
c




25.66
7.079
0
84.95
0
2.654




9.734
7.079
1.769
5.309
29.20
8.849




45.13
58.40
1.769
0.884
70.79
1.769




19.46
27.43
96.46
8.849
0
86.72



111
g
a
c
a
g
c




11.71
36.03
7.207
99.09
23.42
19.81




3.603
6.306
2.702
0
9.009
3.603




79.27
29.72
6.306
0.900
38.73
34.23




5.405
27.92
83.78
0
28.82
42.34



108
g
g
c
a
g
c




1.851
19.44
37.03
95.37
20.37
4.629




1.851
14.81
4.629
2.777
29.62
3.703




96.29
62.03
6.481
0.925
42.59
25




0
3.703
51.85
0.925
7.407
66.66



95
c
t
g
g
c
c




1.052
1.052
9.473
0
4.210
2.105




3.157
48.42
3.157
0
4.210
4.210




2.105
24.21
87.36
100
8.421
23.15




93.68
26.31
0
0
83.15
70.52



94
c
a
g
g
c
c




4.255
39.36
7.446
43.61
6.382
0




15.95
38.29
7.446
2.127
4.255
1.063




37.23
19.14
85.10
50
13.82
0




42.55
3.191
0
4.255
75.53
98.93



86
c
c
c
a
c
c




5.813
10.46
24.41
91.86
27.90
2.325




30.23
33.72
4.651
2.325
1.162
1.162




1.162
2.325
1.162
5.813
10.46
4.651




62.79
53.48
69.76
0
60.46
91.86



83
g
gc
c
g
c
c




1.204
21.68
18.07
24.09
1.204
0




1.204
18.07
16.86
1.204
4.819
3.614




92.77
30.12
10.84
67.46
3.614
8.433




4.819
30.12
54.21
7.228
90.36
87.95



80
c
c
c
g
c
g




1.25
3.75
6.25
2.5
8.75
0




1.25
2.5
17.5
2.5
0
7.5




36.25
8.75
15
92.5
7.5
92.5




61.25
85
61.25
2.5
83.75
0



79
g
t
c
a
c
c




2.531
7.594
11.39
81.01
1.265
1.265




10.12
82.27
1.265
1.265
2.531
1.265




67.08
6.329
36.70
5.063
0
0




20.25
3.797
50.63
12.65
96.20
97.46



79
g
t
c
a
c
c




13.92
3.797
1.265
73.41
5.063
2.531




3.797
58.22
3.797
1.265
3.797
1.265




70.88
37.97
22.78
18.98
12.65
0




11.39
0
72.15
6.329
78.48
96.20



70
a
g
a
ag
ag
c




85.71
4.285
72.85
45.71
31.42
7.142




4.285
0
2.857
0
21.42
1.428




2.857
78.57
15.71
45.71
31.42
8.571




7.142
17.14
8.571
8.571
15.71
82.85



68
g
g
g
a
g
g




48.52
1.470
44.11
97.05
32.35
26.47




1.470
0
0
1.470
1.470
4.411




50
94.11
51.47
1.470
66.17
54.41




0
4.411
4.411
0
0
14.70



67
c
t
c
a
a
g




2.985
16.41
4.477
98.50
62.68
5.970




7.462
53.73
1.492
0
2.985
1.492




8.955
1.492
37.31
0
31.34
92.53




80.59
28.35
56.71
1.492
2.985
0



64
c
t
c
a
g
c




7.812
0
1.562
95.31
7.812
4.687




28.12
71.87
0
0
7.812
1.562




7.812
20.31
0
0
81.25
1.562




56.25
7.812
98.43
4.687
3.125
92.18



62
a
g
c
a
t
c




95.16
12.90
9.677
74.19
9.677
0




1.612
27.41
11.29
1.612
87.09
0




3.225
35.48
12.90
22.58
1.612
0




0
24.19
66.12
1.612
1.612
100



61
g
c
g
g
c
c




8.196
1.639
3.278
1.639
1.639
0




4.918
3.278
27.86
1.639
1.639
0




78.68
0
54.09
68.85
0
11.47




8.196
95.08
14.75
27.86
96.72
88.52



61
g
c
a
g
a
g




21.31
3.278
91.80
11.47
63.93
6.557




27.86
0
0
1.639
3.278
11.47




34.42
4.918
3.278
85.24
6.557
81.96




16.39
91.80
4.918
1.639
26.22
0



55
g
g
g
a
c
c




0
1.818
12.72
94.54
21.81
3.636




3.636
1.818
5.454
0
3.636
0




94.54
94.54
41.81
5.454
1.818
5.454




1.818
1.818
40
0
72.72
90.90



52
g
c
a
g
a
g




1.923
1.923
84.61
0
76.92
5.769




1.923
3.846
1.923
0
9.615
3.846




57.69
3.846
3.846
98.07
11.53
86.53




38.46
90.38
9.615
1.923
1.923
3.846



50
t
c
t
g
ag
c




6
4
0
16
36
2




68
2
98
0
12
6




6
8
0
84
36
6




20
86
2
0
16
86



46
g
c
a
g
c
t




0
10.86
97.82
0
6.521
10.86




2.173
21.73
0
0
10.86
54.34




97.82
17.39
2.173
89.13
8.695
30.43




0
50
0
10.86
73.91
4.347



42
g
c
c
a
c
c




19.04
38.09
19.04
95.23
35.71
2.380




0
2.380
26.19
2.380
4.761
2.380




78.57
14.28
9.523
2.380
11.90
0




2.380
45.23
45.23
0
47.61
95.23



42
g
c
c
a
c
a




2.380
4.761
2.380
100
38.09
88.09




0
21.42
2.380
0
2.380
7.142




97.61
2.380
2.380
0
0
4.761




0
71.42
92.85
0
59.52
0



41
t
c
a
g
t
c




0
0
46.34
17.07
14.63
0




90.24
0
41.46
0
58.53
0




2.439
2.439
4.878
80.48
0
0




7.317
97.56
7.317
2.439
26.82
100



41
c
c
c
a
c
c




0
12.19
2.439
78.04
4.878
2.439




0
19.51
2.439
2.439
0
14.63




2.439
24.39
0
19.51
0
7.317




97.56
43.90
95.12
0
95.12
75.60



40
t
t
c
a
a
g




5
0
5
100
50
0




65
95
0
0
2.5
5




0
2.5
10
0
47.5
87.5




30
2.5
85
0
0
7.5



38
c
c
c
a
a
a




0
0
2.631
94.73
57.89
55.26




2.631
23.68
0
0
10.52
0




5.263
0
10.52
5.263
10.52
39.47




92.10
76.31
86.84
0
21.05
5.263

















TABLE 4





Emerging gene clusters which were identified by the clustering method pertaining Bos Tauros.


The below clusters are arranged according to declining size. For each cluster, the table depicts


the distribution of nucleotides for each position along the context sequence.
















Size of










Cluster

Distribution of nucleotides per position


(number of
Function attributes set (Enrichment
along the context sequence (%)












genes)
score/P_value/Benjamini)
Pos:
−9
−8
−7





815
structural molecule activity (2.4, 6.1E−5, 7.0E−2);

g
c
c



structural constituent of ribosome (2.4, 8.6E−5, 5.0E−2);
A %
11.77
7.975
10.30



ribosome (2.4, 3.4E−4, 8.5E−2); ribosomal protein (2.4,
T %
9.079
8.343
14.72



4.9E−4, 2.0E−1); ribonucleoprotein complex (2.4, 1.1E−3,
G %
63.55
22.45
20.73



1.4E−1); membrane (1.3, 4.8E−3, 3.9E−1); regulation of
C %
15.58
61.22
54.23



signal transduction (1.03, 4.0E−3, 6.9E−1); regulation of



signal transduction (0.87, 4.0E−3, 6.9E−1); intracellular



non-membrane-bound organelle (0.79, 2.9E−3, 2.3E−1);



non-membrane-bound organelle (0.79, 2.9E−3, 2.3E−1);



lipoprotein (0.4, 6.9E−3, 4.4E−1);


583
intracellular non-membrane-bound organelle (1.78, 5.5E−3,

g
c
c



5.2E−1); non-membrane-bound organelle (1.78, 5.5E−3,
A %
10.29
7.375
8.404



5.2E−1); ribosome (1.78, 8.9E−3, 5.5E−1); pyridoxal
T %
10.46
18.86
15.95



phosphate (1.23, 6.3E−3, 4.8E−1); homodimer (1.11,
G %
49.91
20.75
27.95



1.6E−3, 2.5E−1); membrane (1.07, 8.7E−4, 2.3E−1);
C %
29.33
53.00
47.68



glycoprotein (1.07, 1.3E−2, 6.2E−1); eye lens protein



(1.03, 6.1E−3, 5.1E−1); kinase (0.69, 1.1E−2, 6.0E−1);



cytoplasm (0.65, 1.5E−2, 6.4E−1); transit peptide (0.4,



7.5E−3, 5.0E−1);


474
Cathelicidin (2.77, 9.5E−6, 2.7E−2); antibiotic (2.77,

c
c
c



2.3E−4, 1.0E−1); antimicrobial (2.77, 5.7E−4, 1.0E−1);
A %
24.26
3.797
13.08



pyrrolidone carboxylic acid (2.77, 2.0E−3, 2.7E−1);
T %
15.18
18.35
13.50



fungicide (2.77, 8.2E−3, 6.6E−1); nucleotide-binding
G %
18.14
36.28
21.51



(1.68, 1.5E−4, 1.3E−1); signal (0.96, 4.2E−4, 1.2E−1);
C %
42.40
41.56
51.89


463
cellular macromolecule metabolism (2.17, 6.4E−4, 6.1E−1);

g
c
c



cellular physiological process (2.17, 7.0E−4, 4.0E−1);
A %
8.639
3.239
9.503



cellular protein metabolism (2.17, 1.1E−3, 4.0E−1);
T %
4.319
3.455
10.79



protein metabolism (2.17, 1.6E−3, 4.5E−1); structural
G %
68.25
20.73
19.43



molecule activity (1.74, 1.7E−4, 1.9E−1); intracellular
C %
18.79
72.57
60.25



non-membrane-bound organelle (1.74, 1.9E−3, 4.0E−1);



non-membrane-bound organelle (1.74, 1.9E−3, 4.0E−1);



cellular physiological process (1.47, 7.0E−4, 4.0E−1);



structural molecule activity (1.32, 1.7E−4, 1.9E−1);



intracellular non-membrane-bound organelle (1.32, 1.9E−3,



4.0E−1); non-membrane-bound organelle (1.32, 1.9E−3,



4.0E−1); homodimer (1.14, 2.2E−3, 6.4E−1); protein



polymerization (0.92, 2.0E−3, 4.5E−1); cytoskeleton



(0.92, 1.1E−2, 6.2E−1);


300
transit peptide (2, 8.4E−6, 7.7E−3); transit

g
g
a



peptide: Mitochondrion (2, 4.2E−4, 4.2E−1);
A %
17.66
14.33
53



mitochondrion (2, 1.8E−3, 4.3E−1); ubiquinone (2, 3.2E−3,
T %
12
4
5



5.2E−1); oxidoreductase (2, 3.3E−3, 4.5E−1);
G %
51.66
70.33
21.66



intracellular membrane-bound organelle (1.75, 1.8E−3,
C %
18.66
11.33
20.33



3.8E−1); membrane-bound organelle (1.75, 1.9E−3, 2.2E−1);



cytoplasm (1.75, 3.5E−3, 2.7E−1); intracellular



organelle (1.75, 6.8E−3, 3.6E−1); organelle (1.75, 7.2E−3,



3.2E−1); membrane (0.8, 7.3E−3, 6.8E−1);


289
glycoprotein (2.82, 3.1E−4, 2.5E−1); signal (2.82, 4.9E−4,

g
a
a



2.0E−1); disulfide bond (2.82, 5.7E−4, 5.2E−1);
A %
28.37
52.24
47.75



Propeptide, peptidase A1 (2.62, 1.6E−4, 3.8E−1);
T %
13.14
14.87
13.14



Peptidase aspartic, active site (2.62, 4.5E−4, 4.8E−1);
G %
44.29
12.11
21.45



pepsin A activity (2.62, 7.7E−4, 6.0E−1); aspartic-type
C %
14.18
20.76
17.64



endopeptidase activity (2.62, 1.0E−3, 4.6E−1); duplication



(1.45, 1.7E−3, 3.2E−1); cytokine (0.5, 7.9E−4, 2.2E−1);


223
signal (1.73, 5.3E−4, 3.9E−1); structural constituent of

g
c
c



ribosome (1.21, 4.7E−4, 4.3E−1); ribosome (1.21, 1.3E−3,
A %
16.59
5.381
12.55



2.8E−1); ribonucleoprotein complex (1.21, 1.7E−3, 2.0E−1);
T %
6.726
7.623
11.65



ribosomal protein (1.21, 1.9E−3, 5.9E−1);
G %
56.50
23.76
4.035




C %
20.17
63.22
71.74


215
cellular physiological process (1.64, 2.2E−3, 6.6E−1);

g
c
c



cellular process (1.64, 2.4E−3, 5.9E−1); cellular protein
A %
2.325
1.395
5.116



metabolism (1.64, 3.2E−3, 6.1E−1); coated vesicle
T %
0.930
2.325
6.511



membrane (1.43, 7.3E−3, 3.8E−1); vesicle coat (1.43,
G %
90.69
2.790
24.65



7.3E−3, 3.8E−1); membrane coat (1.43, 7.3E−3, 3.8E−1);
C %
6.046
93.48
63.72



coated membrane (1.43, 7.3E−3, 3.8E−1); vesicle



membrane (1.43, 8.8E−3, 3.2E−1); cytoplasmic vesicle



membrane (1.43, 8.8E−3, 3.2E−1); coated vesicle (1.43,



1.2E−2, 3.7E−1); cytoplasmic membrane-bound vesicle



(1.43, 2.2E−2, 5.1E−1); vesicle (1.43, 2.2E−2, 5.1E−1);



membrane-bound vesicle (1.43, 2.2E−2, 5.1E−1);



cytoplasmic vesicle (1.43, 2.2E−2, 5.1E−1); cytoskeleton



(1.35, 3.6E−2, 5.0E−1); microtubule cytoskeleton (1.35,



4.9E−2, 5.8E−1); cellular physiological process (0.95,



2.2E−3, 6.6E−1); cellular process (0.95, 2.4E−3, 5.9E−1);



intracellular non-membrane-bound organelle (0.83, 3.4E−2,



5.3E−1); non-membrane-bound organelle (0.83, 3.4E−2,



5.3E−1):


213
signal (2.88, 2.8E−7, 2.6E−4); glycoprotein (2.88, 2.1E−5,

c
a
g



9.6E−3); membrane (2.88, 1.1E−4, 3.3E−2);
A %
18.30
39.43
18.77



transmembrane (2.88, 2.2E−3, 3.9E−1);
T %
11.73
15.49
6.103




G %
19.24
28.63
70.42




C %
50.70
16.43
4.694


84
nucleotide-binding (1.14, 2.2E−4, 1.8E−1); atp-binding

a
c
c



(1.14, 1.2E−3, 4.2E−1);
A %
66.66
2.380
5.952




T %
10.71
3.571
1.190




G %
3.571
44.04
19.04




C %
19.04
50
73.80


66
membrane-bound organelle (1.11, 7.9E−3, 6.5E−1);

g
g
a




A %
21.21
13.63
68.18




T %
15.15
3.030
9.090




G %
33.33
43.93
22.72




C %
30.30
39.39
0


52
nad (1.73, 1.2E−3, 6.7E−1);

g
t
c




A %
3.846
25
21.15




T %
7.692
40.38
7.692




G %
67.30
28.84
34.61




C %
21.15
5.769
36.53


33
ribonucleoprotein complex (1.11, 1.2E−2, 6.7E−1);

g
c
c




A %
15.15
6.060
21.21




T %
0
0
15.15




G %
78.78
0
0




C %
6.060
93.93
63.63


32
Cathelicidin (3.99, 8.6E−10, 2.5E−6); antibiotic (3.99,

c
g
g



2.6E−7, 2.4E−4); antimicrobial (3.99, 4.6E−7, 2.1E−4);
A %
0
3.125
0



pyrrolidone carboxylic acid (3.99, 1.1E−6, 3.4E−4);
T %
0
31.25
6.25




G %
0
40.62
56.25




C %
100
25
37.5


30
Lipid-binding serum glycoprotein (0.94, 2.5E−4, 5.2E−1);

c
a
g




A %
20
40
0




T %
3.333
30
0




G %
0
23.33
96.66




C %
76.66
6.666
3.333


29
Cathelicidin (5.17, 1.6E−11, 4.6E−8); pyrrolidone

c
t
c



carboxylic acid (5.17, 3.5E−9, 3.2E−6); antibiotic (5.17,
A %
6.896
0
0



3.8E−8, 1.8E−5); antimicrobial (5.17, 7.9E−8, 2.4E−5);
T %
20.68
96.55
13.79



SF001637: cathelin (5.17, 2.3E−4, 2.1E−1); signal (5.17,
G %
3.448
3.448
41.37



4.9E−4, 1.1E−1);
C %
68.96
0
44.82













Size of




Cluster
Distribution of nucleotides per position



(number of
along the context sequence (%)















genes)
−6
−5
−4
−3
−2
−1







815
g
c
c
a
c
c




7.361
9.202
15.70
66.01
24.66
3.190




15.21
14.72
2.453
1.349
7.361
2.576




51.77
32.51
21.10
30.06
32.63
46.38




25.64
43.55
60.73
2.576
35.33
47.85



583
g
c
c
g
c
c




9.777
4.459
27.78
26.07
3.945
1.715




13.37
10.46
3.602
0.686
6.861
3.602




65.00
21.09
10.97
70.32
1.886
8.747




11.83
63.97
57.63
2.915
87.30
85.93



474
gc
g
c
a
c
c




23.62
10.54
8.016
55.27
3.797
3.375




11.81
15.82
8.438
3.797
2.531
4.008




32.27
40.08
18.35
36.70
6.962
4.008




32.27
33.54
65.18
4.219
86.70
88.60



463
g
c
c
g
c
c




7.343
2.807
39.95
20.51
4.967
0.431




3.239
3.671
1.943
0.863
5.615
1.295




76.88
36.28
5.399
77.53
6.479
3.455




12.52
57.23
52.69
1.079
82.93
94.81



300
g
g
c
a
a
g




14.33
21
24
87
69.66
11.33




6.666
6.666
2
0.333
4
2




63.66
40
32.33
11.33
19.33
63.33




15.33
32.33
41.66
1.333
7
23.33



289
a
g
a
a
a
c




48.09
15.91
42.90
93.77
40.13
31.48




22.49
24.91
5.882
0.692
7.266
5.882




22.83
40.48
9.342
4.152
28.71
22.14




6.574
18.68
41.86
1.384
23.87
40.48



223
g
c
c
a
g
g




3.587
1.345
1.345
95.96
28.69
4.484




14.34
4.932
1.345
0.448
7.174
1.793




56.05
33.63
4.484
2.242
62.33
57.39




26.00
60.08
92.82
1.345
1.793
36.32



215
g
c
c
g
c
c




3.720
3.255
17.67
28.83
1.395
0.465




1.395
4.186
0
0
1.860
0.930




90.69
35.81
5.116
70.69
2.325
5.116




4.186
56.74
77.20
0.465
94.41
93.48



213
g
a
c
a
g
c




40.84
41.31
8.450
94.36
23.94
10.79




6.572
29.57
0.469
0.469
27.69
2.816




43.19
25.82
35.21
0.469
32.39
32.86




9.389
3.286
55.86
4.694
15.96
53.52



84
a
g
c
a
c
c




78.57
3.571
1.190
92.85
4.761
8.333




14.28
1.190
0
0
5.952
3.571




4.761
84.52
3.571
3.571
19.04
2.380




2.380
10.71
95.23
3.571
70.23
85.71



66
g
g
g
a
a
g




6.060
0
9.090
95.45
93.93
3.030




0
7.575
0
0
0
1.515




86.36
89.39
46.96
4.545
1.515
90.90




7.575
3.030
43.93
0
4.545
4.545



52
c
c
a
g
c
c




1.923
5.769
38.46
0
19.23
5.769




5.769
0
23.07
0
0
0




0
0
28.84
92.30
11.53
0




92.30
94.23
9.615
7.692
69.23
94.23



33
g
c
c
a
g
c




0
0
0
93.93
6.060
12.12




0
3.030
0
0
39.39
6.060




100
0
0
0
54.54
0




0
96.96
100
6.060
0
81.81



32
g
g
g
g
c
c




3.125
6.25
15.62
40.62
6.25
0




0
0
3.125
0
0
3.125




96.87
93.75
81.25
59.37
0
3.125




0
0
0
0
93.75
93.75



30
g
a
gc
a
a
g




30
86.66
0
100
96.66
0




3.333
10
0
0
0
0




66.66
0
50
0
3.333
100




0
3.333
50
0
0
0



29
g
g
c
a
c
c




6.896
3.448
24.13
96.55
3.448
3.448




0
0
0
0
0
0




93.10
93.10
24.13
0
3.448
0




0
3.448
51.72
3.448
93.10
96.55










REFERENCES


    1 Everitt. B., Cluster Analysis, Edward Arnold, London, 1993
    1 W. Thong, G. Altun, R. Harrison, P. C. Tai, and Y. Pan, Improved K-Means Clustering Algorithm for Exploring Local Protein Sequence Motifs, Representing. Common Structural Property, IEEE TRANSACTIONS ON NANOBIOSCIENCE, VOL. 4, NO. 3, SEPTEMBER 2005.
    1 K. F. Han, D. Baker, Recurring local sequence motifs in proteins J. Mol. Biol., vol. 251(1), pages 176-187, 1995
    1 Heidecker G, Messing J: Structural analysis of plant genes. Annu. Rev. Plant Physiol. 37, 439-466 (1986)
    1 C. P. Joshi, An Inspection of the domain putative An inspection of the domain between putative TATA box and translation start site in 79 plant genes, Nucleic Acids Research, 1987, Vol. 15, No. 16 6643-6653.
    1 C. P. Joshi, H. Thou, X. Huang and V. L. Chiang, Context sequences of translation initiation codon in plants, Plant Molecular Biology 35: 993-1001, 1997; Q. Liu, Q. Xue, Comparative studies on sequence characteristics around translation initiation codon in four eukaryotes, Journal of Genetics, Vol. 84, No. 3, December 2005.
    1 M. Jaiswal, L. Rangan, Context Sequence For Transcription Factors Surrounding Start Codon in Model Crops, CURRENT SCIENCE, VOL. 93, NO. 2, 25 Jul. 2007.
    1 Kozak M. Nucleotide sequences of 5′-terminal ribosome-protected initiation regions from two reovirus messages. Nature. 1977 Sep. 29; 269(5627):391-4; Kozak M. Possible role of flanking nucleotides in recognition of the AUG initiator codon by eukaryotic ribosomes. Nucleic Acids Res. 1981 Oct. 24; 9(20):5233-52.; Kozak M. Sequences of ribosome binding sites from the large size class of reovirus mRNA. J. Virol. 1982 May; 42(2):467-73
    1 Compilation and analysis of sequences upstream from the translational start site in eukaryotic mRNAs. Nucleic Acids Res. 1984 Jan. 25; 12(2):857-72.; Kozak M: An analysis of 50-noncoding sequences from 699 vertebrate messenger RNAs. Nucl Acids Res 15, 8125-8148 (1987); Kozak M: At least six nucleotides preceding the AUG initiator codon enhance translation in mammalian cells. J Mol Biol 196: 947-950 (1987).
    1 Samir V. S., Pradhyumna K. S., Shiv K. G., Raju M. and Rakesh T, Conserved nucleotide sequences in highly expressed genes in plants, Journal of Genetics, Vol. 78, No. 2, August 1999 123.
    1 Taylor J L, Jones J D G, Sandler S, Mueller G M, Bedbrook J, Dunsmuir, Optimizing the Expression of Chimeric Genes in Plant Cells, Mol. Gen. Genet. (1987)210, pages 572-577.
    1 Sleat D. E., Gallie D. R, Jefferson R. A., Bevan M. W., Turner P. C., Wilson T. M. A., Characterization of the 50-leader Sequence of Tobacco Mosaic Virus RNA as a General Enhancer of Translation in vitro, Gene (1987)217: 217-225.
    1 Chandrashekhar P. Joshi, Hao Zhou, Xiaoqiu Huang and Vincent L. Chiang, Context sequences of translation initiation codon in plants, Plant Molecular Biology 35: 993-1001, 1997, at p. 998 below.
    1 C. P. Joshi, H. Zhou, X. Huang and V. L. Chiang, Context sequences of translation initiation codon in plants, Plant Molecular Biology (1997)35: 993-1001, see Table 3 at p. 1000.
    1 See for example U.S. Pat. No. 7,253,342.
    1 D. Arthur, S. Vassilvitskii, How Slow is the k—Means Method?, 2006 (Stanford, yet unpublished). See www.stanford.edu/ ̃sergeiv/papers/ldVIeans-socg.pdf
    1 Thomas H. Cormen, Charles E. Leiserson, Ronald L. Rivest (1990): Introduction to algorithms. MIT Press/McGraw-Hill.
    1 Dennis G Jr, Sherman B T, Hosack D A, Yang J, Gao W, Lane H C, Lempicki R A. DAVID: Database for Annotation, Visualization, and Integrated Discovery. Genome Biology 2003, 4(5).
    1 D. A Hosack, G. D. Jr, B. T Sherman, H C. Lane, R. A Lempicki. Identifying Biological Themes within Lists of Genes with EASE. Genome Biology 2003 4(6).
    1 Dennis G Jr, Sherman B T, Hosack D A, Yang J, Gao W, Lane H C, Lempicki R A. DAVID: Database for Annotation, Visualization, and Integrated Discovery. Genome Biology 2003, 4(5).
    1 D. A Hosack, G. D. Jr, B. T Sherman, H C. Lane, R. A Lempicki. Identifying Biological Themes within Lists of Genes with EASE. Genome Biology 2003 4(6).
    1 Chandrashekhar P. Joshi, Hao Zhou, Xiaoqiu Huang and Vincent L. Chiang, Context sequences of translation initiation codon in plants, Plant Molecular Biology 35: 993-1001, 1997.
    1 Chandrashekhar P. Joshi, Hao Thou, Xiaoqiu Huang and Vincent L. Chiang, Context sequences of translation initiation codon in plants, Plant Molecular Biology 35: 993-1001, 1997, at p. 999.

## Claims

1. A computer implemented method for identifying a sequence template as statistically associated with plant functional annotations of interest, the method implemented on a computer comprising a processor, and computer readable memory comprising RAM and secondary storage, the method comprising:
(a) obtaining, using the processor, a first plant functional annotation set comprising at least one plant functional annotation from a user;
(b) obtaining, using the processor, a data repository comprising polynucleotide plant mRNA sequences and storing the data repository in the computer readable memory; and
(c) for each mRNA sequence, identifying, using the processor, the translation initiation codon and a corresponding context sequence comprising a stretch of nucleotides preceding the translation initiation codon;
(d) transforming, using the processor, each of the context sequences into a sequence template;
(e) allocating, in the computer readable memory, a multiple-tree-array data structure, the multiple-tree-array consisting of a root node and a plurality of heaps, at least one of the heaps being stored in the RAM and at least one of the heaps being stored in the secondary storage;
(f) inserting, using the processor, data items into the multiple-tree-array, the data items comprising two sequence templates and a distance between the sequence templates;
(g) clustering, using the processor, the sequence templates, wherein the clustering comprises retrieving data items from the multiple-tree-array, storing data items in the multiple-tree-array, and merging the sequence templates in a cluster into a common sequence template that represents all of the templates within the cluster;
(h) selecting, using the processor, a cluster;
(i) obtaining, using the processor, a list of plant functional annotations that are statistically overrepresented within said cluster; and
(j) storing the sequence template and the functional annotations of said cluster in the computer readable memory.

2. The computer implemented method of claim 1, wherein the corresponding context sequence is a stretch of 9 or 10 nucleotides preceding the translation initiation codon.

3. The computer implemented method of claim 1, said attributes are selected from: the Gene Ontology Project (GO), Interpro annotation (European Molecular Biology Laboratory, EMBL), SMART (a Simple Modular Architecture Research Tool), UniProt Knowledgebase (SwissProt), OMIM (by NCBI) PROSITE (by the Swiss Institute of Bioinformatics), Protein Information Resource (PIR), GeneCards, and Kyoto Encyclopedia of Genes and Genomes (KEGG).

4. The computer implemented method of claim 1, wherein step (c) further includes the step of aligning the context sequences of the polynucleotide plant mRNA sequences.

5. The computer implemented method of claim 1, wherein the sequence template is a distribution matrix representing the distribution of each nucleotide for each nucleotide position which characterizes the corresponding context sequence.

6. The computer implemented method of claim 5, wherein the distribution matrix is paired to the first plant functional annotation set comprising at least one plant functional annotation.

7. The computer implemented method of claim 6, further comprising allocating a tabular memory structure comprising table rows, wherein the table rows comprise data including the distribution matrix representing the sequence template and the associated plant functional annotations and wherein a user interface provides for a user to enter a desired importance degree or confidence level associated with a particular function attribute.

8. The computer implemented method of claim 7, wherein the data repository is RefSeq.

9. The computer implemented method of claim 1, wherein the data repository comprising polynucleotide plant mRNA sequences is curated.

10. The computer implemented method of claim 1, wherein the retrieval of data items from the multiple-tree-array and storage of data items in the multiple-tree-array are managed through a common interface such that at least one of the heaps maintained in the RAM can be replaced with at least one heap maintained in the secondary storage.