bluuebunny/crossref_metadata_2025_split huggingface dataset:
MetaFam: a unified classification of protein families. I.

Overview and statistics
Authors: Silverstein Kevin A. T. , Shoop Elizabeth , Johnson James E. , Retzel Ernest F. 
Published: July 2002

Abstract
Motivation: Protein sequence classification is becoming an increasingly important means of organizing the voluminous data produced by large-scale genome sequencing projects. At present, there are several independent classification methods. To aid the general classification effort, we have created a unified protein family resource, MetaFam. MetaFam is a protein family classification built upon 10 publicly-accessible protein family databases (Blocks\batchmode \documentclass[fleqn,10pt,legalpaper]{article} \usepackage{amssymb} \usepackage{amsfonts} \usepackage{amsmath} \pagestyle{empty} \begin{document} \(+\) \end{document}, DOMO, Pfam, PIR-ALN, PRINTS, PROSITE, ProDom, PROTOMAP, SBASE, and SYSTERS). MetaFam’s family ‘supersets’, as we call them, are created automatically using set-theory to compare families among the databases. Families of one database are matched to those in another when the intersection of their members exceeds all other possible family pairings between the two databases. Pairwise family matches are drawn together transitively to create a new list of protein family supersets.
Results: MetaFam family supersets have several useful features: (1) each superset contains more members than the families from which it is composed, because each of the component family databases only works with a subset of our full non-redundant set of proteins; (2) conflicting assignments can be pinpointed quickly, since our analysis identifies individual members that are in conflict with the majority consensus; (3) family descriptions that are absent from automated databases can frequently be assigned; (4) statistics have been computed comparing domain boundaries, family size distributions, and overall quality of MetaFam supersets; (5) the supersets have been loaded into a relational database to allow for complex queries and visualization of the connections among families in a superset and the consensus of individual domain members; and (6) the quality of individual supersets has been assessed using numerous quantitative measures such as family consistency, connectedness, and size. We anticipate this new resource will be particularly useful to genomic database curators.
Availability: Free access to the MetaFam web server is provided to all users at http://metafam.ahc.umn.edu/.
Contact: metafam@ahc.umn.edu
Supplementary information: Detailed distribution plots on MetaFam 2.0 supersets and its constituent family databases (e.g. superset/family sizes, domain boundary comparisons) are shown at http://metafam.ahc.umn.edu/mf2.0/stats.html. Statistics on the current release of MetaFam can be found at http://metafam.ahc.umn.edu/current_release/stats.html.
* To whom correspondence should be addressed.
A new approach to sequence comparison: normalized sequence
alignment
Authors: Arslan Abdullah N. , Eğecioğlu Ömer , Pevzner Pavel A. 
Published: July 2002

Abstract
The Smith–Waterman algorithm for local sequence alignment is one of the most important techniques in computational molecular biology. This ingenious dynamic programming approach was designed to reveal the highly conserved fragments by discarding poorly conserved initial and terminal segments. However, the existing notion of local similarity has a serious flaw: it does not discard poorly conserved intermediate segments. The Smith–Waterman algorithm finds the local alignment with maximal score but it is unable to find local alignment with maximum degree of similarity (e.g. maximal percent of matches). Moreover, there is still no efficient algorithm that answers the following natural question: do two sequences share a (sufficiently long) fragment with more than 70% of similarity? As a result, the local alignment sometimes produces a mosaic of well-conserved fragments artificially connected by poorly-conserved or even unrelated fragments. This may lead to problems in comparison of long genomic sequences and comparative gene prediction as recently pointed out by Zhang et al. (Bioinformatics , 15, 1012–1019, 1999). In this paper we propose a new sequence comparison algorithm (normalized local alignment ) that reports the regions with maximum degree of similarity. The algorithm is based on fractional programming and its running time is \batchmode \documentclass[fleqn,10pt,legalpaper]{article} \usepackage{amssymb} \usepackage{amsfonts} \usepackage{amsmath} \pagestyle{empty} \begin{document} \(O(n^{2}\mathrm{log}n)\) \end{document}. In practice, normalized local alignment is only 3–5 times slower than the standard Smith–Waterman algorithm.
Contact: {arslan,omer}@cs.ucsb.edu; ppevzner@cs.ucsd.edu
NIFAS: visual analysis of domain evolution in proteins
Authors: Storm Christian E. V. , Sonnhammer Erik L. L. 
Published: July 2002

Abstract
Motivation: Multi-domain proteins have evolved by insertions or deletions of distinct protein domains. Tracing the history of a certain domain combination can be important for functional annotation of multi-domain proteins, and for understanding the function of individual domains. In order to analyze the evolutionary history of the domains in modular proteins it is desirable to inspect a phylogenetic tree based on sequence divergence with the modular architecture of the sequences superimposed on the tree.
Result: A Java applet, NIFAS, that integrates graphical domain schematics for each sequence in an evolutionary tree was developed. NIFAS retrieves domain information from the Pfam database and uses CLUSTAL W to calculate a tree for a given Pfam domain. The tree can be displayed with symbolic bootstrap values, and to allow the user to focus on a part of the tree, the layout can be altered by swapping nodes, changing the outgroup, and showing/collapsing subtrees. NIFAS is integrated with the Pfam database and is accessible over the internet (http://www.cgr.ki.se/Pfam). As an example, we use NIFAS to analyze the evolution of domains in Protein Kinases C.
Contact: christian.storm@cgr.ki.se
Construction of DNA restriction maps based on a simplified

experiment
Authors: Błażewicz J. , Formanowicz P. , Kasprzak M. , Jaroszewski M. , Markiewicz W. T. 
Published: July 2002

Abstract
Motivation: A formulation of a new problem of the restriction map construction based on a simplified digestion experiment and a development of an algorithm for solving both ideal and noisy data cases of the introduced problem.
Results: A simplified partial digest problem and a branch and cut algorithm for finding the solution of the problem.
Contact: blazewic@sol.put.poznan.pl
* To whom correspondence should be addressed.
† Fellowship holder of the Foundation for Polish Sciences.
SVDMAN—singular value decomposition analysis of

microarray data
Authors: Wall Michael E. , Dyck Patricia A. , Brettin Thomas S. 
Published: July 2002

Abstract
Summary: We have developed two novel methods for Singular Value Decomposition analysis (SVD) of microarray data. The first is a threshold-based method for obtaining gene groups, and the second is a method for obtaining a measure of confidence in SVD analysis. Gene groups are obtained by identifying elements of the left singular vectors, or gene coefficient vectors, that are greater in magnitude than the threshold \batchmode \documentclass[fleqn,10pt,legalpaper]{article} \usepackage{amssymb} \usepackage{amsfonts} \usepackage{amsmath} \pagestyle{empty} \begin{document} \(WN^{{-}1/2}\) \end{document}, where \batchmode \documentclass[fleqn,10pt,legalpaper]{article} \usepackage{amssymb} \usepackage{amsfonts} \usepackage{amsmath} \pagestyle{empty} \begin{document} \(N\) \end{document}is the number of genes, and \batchmode \documentclass[fleqn,10pt,legalpaper]{article} \usepackage{amssymb} \usepackage{amsfonts} \usepackage{amsmath} \pagestyle{empty} \begin{document} \(W\) \end{document}is a weight factor whose default value is 3. The groups are non-exclusive and may contain genes of opposite (i.e. inversely correlated) regulatory response. The confidence measure is obtained by systematically deleting assays from the data set, interpolating the SVD of the reduced data set to reconstruct the missing assay, and calculating the Pearson correlation between the reconstructed assay and the original data. This confidence measure is applicable when each experimental assay corresponds to a value of parameter that can be interpolated, such as time, dose or concentration. Algorithms for the grouping method and the confidence measure are available in a software application called SVD Microarray ANalysis (SVDMAN). In addition to calculating the SVD for generic analysis, SVDMAN provides a new means for using microarray data to develop hypotheses for gene associations and provides a measure of confidence in the hypotheses, thus extending current SVD research in the area of global gene expression analysis.
Availability: ftp://bpublic.lanl.gov/compbio/software
Contact: brettin@lanl.gov
Supplementary information: http://home.lanl.gov/svdman
* To whom correspondence should be addressed.
LDB2000: sequence-based integrated maps of the human genome
Authors: Ke Xiayi , Tapper William , Collins Andrew 
Published: July 2002

Abstract
Motivation: Integrated maps are useful for gene mapping and establishing the relationship between recombination and sequence. In this paper we describe algorithms and their implementation for constructing sequence-based integrated maps of the human chromosomes, which are presented in LDB2000, a web based resource. Gene mapping efforts are now focussing on linkage disequilibrium mapping and extension of the integrated map to represent the extent of linkage disequilibrium in different genomic regions would further increase the utility of these maps.
Results: Sequence-based integrated maps have been completed for chromosomes 21 and 22. These maps provide locations for genes and polymorphic markers in sequence and on genetic linkage, radiation hybrid and cytogenetic scales. Single nucleotide polymorphisms associated with genes in the maps are also included and their sequence locations indicated. Related locus information, such as aliases and expression information, can be searched on the WWW site.
Availability: http://cedar.genetics.soton.ac.uk/public_html/LDB2000.html
Contact: arc@soton.ac.uk
MEDUSA: large scale automatic selection and visual assessment
of PCR primer pairs
Authors: Podowski Raf M. , Sonnhammer Erik L. L. 
Published: July 2002

Abstract
Summary: MEDUSA is a tool for automatic selection and visual assessment of PCR primer pairs, developed to assist large scale gene expression analysis projects. The system allows specification of constraints of the location and distances between the primers in a pair. For instance, primers in coding, non-coding, exon/intron-spanning regions might be selected. Medusa applies these constraints as a filter to primers predicted by three external programs, and displays the resulting primer pairs graphically in the Blixem (Sonnhammer and Durbin, Comput. Appl. Biosci.10, 301–307, 1994; http://www.cgr.ki.se/cgr/groups/sonnhammer/Blixem.html) viewer.
Availability: The MEDUSA web server is available at http://www.cgr.ki.se/cgr/MEDUSA. The source code and user information are available at ftp://ftp.cgr.ki.se/pub/prog/medusa.
Contact: Erik.Sonnhammer@cgr.ki.se
Representation of amino acids as five-bit or three-bit patterns
for filtering protein databases
Authors: Coghlan Avril , Mac
   Dónaill Dónall A. , Buttimore Nigel H. 
Published: July 2002

Abstract
Motivation: We propose representing amino acids by bit-patterns so they may be used in a filter algorithm for similarity searches over protein databases, to rapidly eliminate non-homologous regions of database sequences. The filter algorithm would be based on dynamic programming optimization. It would have the advantage over previous filter algorithms that its substitution scoring function distinguishes between conservative and non-conservative amino acid substitutions.
Results: Simulated annealing was used to search for the best five-bit or three-bit patterns to represent amino acids, where similar amino acids were given similar bit-patterns. The similarity between amino acids was estimated from the BLOSUM45 matrix. Representing amino acids by these five-bit and three-bit patterns, the Escherichia coli PhoE precursor and the bacteriophage PA2 LC precursor were aligned. The alignments were nearly the same as that obtained when BLOSUM45 was used to score substitutions.
Availability: The C code of the optimization algorithm for searching for the optimal bit-pattern representation of amino acids is available from the authors upon request.
Contact: dmcdonll@tcd.ie
* To whom correspondence should be addressed.
Amino acid similarity matrices based on force fields
Authors: Dosztányi Zsuzsanna , Torda Andrew E. 
Published: July 2002

Abstract
Motivation: We propose a general method for deriving amino acid substitution matrices from low resolution force fields. Unlike current popular methods, the approach does not rely on evolutionary arguments or alignment of sequences or structures. Instead, residues are computationally mutated and their contribution to the total energy/score is collected. The average of these values over each position within a set of proteins results in a substitution matrix.
Results: Example substitution matrices have been calculated from force fields based on different philosophies and their performance compared with conventional substitution matrices. Although this can produce useful substitution matrices, the methodology highlights the virtues, deficiencies and biases of the source force fields. It also allows a rather direct comparison of sequence alignment methods with the score functions underlying protein sequence to structure threading.
Availability: Example substitution matrices are available from http://www.rsc.anu.edu.au/~zsuzsa/suppl/matrices.html.
Supplementary information: The list of proteins used for data collection and the optimized parameters for the alignment are given as supplementary material at http://www.rsc.anu.edu.au/~zsuzsa/suppl/matrices.html.
Contact: zsuzsa@rsc.anu.edu.au
* To whom correspondence should be addressed.
A fast top–down method for constructing reliable
radiation hybrid frameworks
Authors: Bø Trond H. , Jonassen Inge , Eidhammer Ingvar , Helgesen Carsten 
Published: July 2002

Abstract
Motivation: Radiation Hybrid Mapping (RHM) is a technique used to order a set of markers on a genome and estimating physical distances between them. RHM provides information on marker placement independent from other methods such as sequencing, and can therefore be used for example in genome sequencing to help ordering contigs. A radiation hybrid framework can be constructed by choosing a set of markers so that the chromosome coverage is good and so that the markers can be ordered with high confidence. Automatically constructing RHM frameworks is a computationally challenging problem.
Results: We have developed a new method for constructing radiation hybrid frameworks. Given a relatively large set of markers for a chromosome, the algorithm aims to select an ordered subset that makes up a framework, and that contains as many markers as possible. The algorithm has a time complexity that is better than any of the existing methods that we are aware of. Furthermore, we propose a method for comparing if two frameworks are consistent, giving a visual presentation as well as quantitative measures of how well the two frameworks agree. Applying our method on marker sets from 22 human chromosomes and comparing the resulting frameworks with previously published frameworks, we demonstrate that our automatic method efficiently constructs frameworks with good coverage of each chromosome and with high degree of agreement on the marker ordering.
Availability: The software is available from the authors.
Supplementary information: MCST paths, frameworks and plots are available at http://www.ii.uib.no/~trondb/RHmapping/
Contact: trondb@ii.uib.no
* To whom correspondence should be addressed.
A viral sampling design for testing the molecular clock and for
estimating evolutionary rates and divergence times
Authors: Seo Tae-Kun , Thorne Jeffrey L. , Hasegawa Masami , Kishino Hirohisa 
Published: July 2002

Abstract
Motivation: The high pace of viral sequence change means that variation in the times at which sequences are sampled can have a profound effect both on the ability to detect trends over time in evolutionary rates and on the power to reject the Molecular Clock Hypothesis (MCH). Trends in viral evolutionary rates are of particular interest because their detection may allow connections to be established between a patient’s treatment or condition and the process of evolution. Variation in sequence isolation times also impacts the uncertainty associated with estimates of divergence times and evolutionary rates. Variation in isolation times can be intentionally adjusted to increase the power of hypothesis tests and to reduce the uncertainty of evolutionary parameter estimates, but this fact has received little previous attention.
Results: We provide approximations for the power to reject the MCH when the alternative is that rates change in a linear fashion over time and when the alternative is that rates differ randomly among branches. In addition, we approximate the standard deviation of estimated evolutionary rates and divergence times. We illustrate how these approximations can be exploited to determine which viral sample to sequence when samples representing different dates are available.
Contact: seo@ism.ac.jp; thorne@statgen.ncsu.edu; hasegawa@ism.ac.jp; kishino@wheat.ab.a.u-tokyo.ac.jp
* To whom correspondence should be addressed.
Machine learning of functional class from phenotype data
Authors: Clare Amanda , King Ross D. 
Published: July 2002

Abstract
Motivation: Mutant phenotype growth experiments are an important novel source of functional genomics data which have received little attention in bioinformatics. We applied supervised machine learning to the problem of using phenotype data to predict the functional class of Open Reading Frames (ORFs) in Saccaromyces cerevisiae. Three sources of data were used: TRansposon-Insertion Phenotypes, Localization and Expression in Saccharomyces (TRIPLES), European Functional Analysis Network (EUROFAN) and Munich Information Center for Protein Sequences (MIPS). The analysis of the data presented a number of challenges to machine learning: multi-class labels, a large number of sparsely populated classes, the need to learn a set of accurate rules (not a complete classification), and a very large amount of missing values. We modified the algorithm C4.5 to deal with these problems.
Results: Rules were learnt which are accurate and biologically meaningful. The rules predict function of 83 ORFs of unknown function at an estimated accuracy of ⩾ 80%.
Availability: The data and complete results are available at http://users.aber.ac.uk/ajc99/phenotype/.
Contact: ajc99@aber.ac.uk
Calculating the SNP-effective sample size from an alignment
Authors: Haubold Bernhard , Wiehe Thomas 
Published: July 2002

Abstract
Motivation: The number of Single Nucleotide Polymorphisms (SNPs) detectable in an alignment is a function of the length and the number of the aligned sequences. The latter is called sample size. However, a typical alignment, for instance obtained as a BLAST-search result of a query sequence against an EST database, does not evenly cover the query sequence. Therefore, it is usually not clear what the actual sample size is.
Results: We present a method to calculate the effective sample size, called neff, for a given BLAST alignment. This method takes into account that multiple coverage contributes only logarithmically to the SNP yield of a given sequence stretch. We show that the effective sample size neff is usually much smaller than would be expected for a given amount of coverage and illustrate this with two typical examples.
Availability: The algorithm is implemented in NEFF, a program written in FORTRAN90 that is accessible at http://soft.ice.mpg.de/neff. From this site also the source, except for two subroutines protected by copyright, and a LINUX compiled executable can be downloaded.
Contact: twiehe@ice.mpg.de
* To whom correspondence should be addressed.
2 Present address: LION Bioscience AG, Heidelberg, Germany.
Extracting transcriptional events from temporal gene expression
patterns during Dictyostelium development
Authors: S̆ás̆ik R. , Iranfar N. , Hwa T. , Loomis W. F. 
Published: July 2002

Abstract
Motivation: The DNA microarray technology can generate a large amount of data describing the time-course of gene expression. These data, when properly interpreted, can yield a great deal of information concerning differential gene expression during development. Much current effort in bioinformatics has been devoted to the analysis of gene expression data, usually via some ‘clustering analysis’ on the raw data in some abstract high dimensional space. Here, we describe a method where we first ‘process’ the raw time-course data using a simple biologically based kinetic model of gene expression. This allows us to reduce the vast data to a few vital attributes characterizing each expression profile, e.g. the times of the onset and cessation of the expression of the developmentally regulated genes. These vital attributes can then be trivially clustered by visual inspection to reveal biologically significant effects.
Results: We have applied this approach to microarray expression data from samples isolated every 2 h throughout the 24 h developmental program of Dictyostelium discoideum. mRNA accumulation patterns for 50 developmental genes were found to fit the kinetic model with a p-value of 0.05 or better. Transcription of these genes appears to be initiated in bursts at well-defined periods during development, in a manner suggestive of a dependent sequence. This approach can be applied to analyses of other temporal gene expression patterns, including those of the cell cycle.
Contact: sasik@physics.ucsd.edu
Supplementary information: Intensity ratios for all genes in this study are available at http://www.biology.ucsd.edu/loomis-cgi/microarray/index.html.
* To whom correspondence should be addressed.
MaxBench: evaluation of sequence and structure comparison
methods
Authors: Leplae Raphael , Hubbard Tim J. P. 
Published: July 2002

Abstract
Summary: MaxBench is a web-based system available for evaluating the results of sequence and structure comparison methods, based on the SCOP protein domain classification. The system makes it easy for developers to both compare the overall performance of their methods to standard algorithms and investigate the results of individual comparisons.
Availability: http://www.sanger.ac.uk/Users/lp1/MaxBench/
Contact: lp1@sanger.ac.uk
* To whom correspondence should be addressed.
Extraction of knowledge on protein--protein interaction
by association rule discovery
Authors: Oyama T. , Kitano K. , Satou K. , Ito T. 
Published: July 2002

Abstract
Motivation: Protein--protein interactions are systematically examined using the yeast two-hybrid method. Consequently, a lot of protein--protein interaction data are currently being accumulated. Nevertheless, general information or knowledge on protein--protein interactions is poorly extracted from these data. Thus we have been trying to extract the knowledge from the protein--protein interaction data using data mining.
Results: A data mining method is proposed to discover association rules related to protein--protein interactions. To evaluate the detected rules by the method, a new scoring measure of the rules is introduced. The method allowed us to detect popular interaction rules such as ‘An SH3 domain binds to a proline-rich region.’ These results indicate that the method may detect novel knowledge on protein--protein interactions.
Contact: oyama@isl.intec.co.jp
* To whom correspondence should be addressed.