bluuebunny/crossref_metadata_2025_split huggingface dataset:
On the convergence of a clustering algorithm for protein-coding
regions in microbial genomes
Authors: Baldi Pierre 
Published: July 2002

Abstract
Motivation: As the number of fully sequenced prokaryotic genomes continues to grow rapidly, computational methods for reliably detecting protein-coding regions become even more important. Audic and Claverie (1998) Proc. Natl Acad. Sci. USA , 95, 10026–10031, have proposed a clustering algorithm for protein-coding regions in microbial genomes. The algorithm is based on three Markov models of order k associated with subsequences extracted from a given genome. The parameters of the three Markov models are recursively updated by the algorithm which, in simulations, always appear to converge to a unique stable partition of the genome. The partition corresponds to three kinds of regions: (1) coding on the direct strand, (2) coding on the complementary strand, (3) non-coding.
Results: Here we provide an explanation for the convergence of the algorithm by observing that it is essentially a form of the expectation maximization (EM) algorithm applied to the corresponding mixture model. We also provide a partial justification for the uniqueness of the partition based on identifiability. Other possible variations and improvements are briefly discussed.
Contact: pfbaldi@ics.uci.edu
A browser for expression data
Authors: Pocock M. R. , Hubbard T. J. P. 
Published: July 2002

Abstract
Summary: We have written a fully extensible Java application for visually browsing expression data, and clusters of genes or experimental conditions calculated from that data. The application requires a runtime environment for Java2.
Availability: http://www.sanger.ac.uk/Users/mrp/java/ExpressionBrowser
Contact: mrp@sanger.ac.uk
RSDB: representative protein sequence databases have high
information content
Authors: Park Jong , Holm Liisa , Heger Andreas , Chothia Cyrus 
Published: July 2002

Abstract
Motivation: Biological sequence databases are highly redundant for two main reasons: 1. various databanks keep redundant sequences with many identical and nearly identical sequences 2. natural sequences often have high sequence identities due to gene duplication. We wanted to know how many sequences can be removed before the databases start losing homology information. Can a database of sequences with mutual sequence identity of 50% or less provide us with the same amount of biological information as the original full database?
Results: Comparisons of nine representative sequence databases (RSDB) derived from full protein databanks showed that the information content of sequence databases is not linearly proportional to its size. An RSDB reduced to mutual sequence identity of around 50% (RSDB50) was equivalent to the original full database in terms of the effectiveness of homology searching. It was a third of the full database size which resulted in a six times faster iterative profile searching. The RSDBs are produced at different granularity for efficient homology searching.
Availability: All the RSDB files generated and the full analysis results are available through internet: ftp://ftp.ebi.ac.uk/pub/contrib/jong/RSDB/http://cyrah.ebi.ac.uk:1111/Proj/Bio/RSDB
Contact: jong@biosophy.org
The PACRAT system: an extensible WWW-based system for

correlated sequence retrieval, storage and analysis
Authors: Ray William C. , Daniels Charles J. 
Published: July 2002

Abstract
Summary: With PACRAT (Patterns, Analyses, Correlations. Remote Archive Testbed) we present an online database solution to the problem of accessing high-confidence sequences with specific relationships to classes of genes, such as upstream intergenic regions attached to tRNA genes. In addition the software contains a data warehousing and analysis-facilitating suite to streamline the process of analyzing the collected data. An unexpected additional benefit of the system is that it also provides easy access to sequences of lower confidence, and may be of assistance in such things as resolving ORF-call conflicts in genomic annotation projects.
Availability: An instance of the PACRAT system, implemented on a set of archaeal genomes, an experimental version of a Yeast genome database, and a random sequence database, is available for use at http://www.biosci.ohio-state.edu/~pacrat/. The system is also available for download for installation of local project-oriented sites. See the online PACRAT ‘About’ page for details.
Contact: ray@biosci.ohio-state.edu; daniels.7@osu.edu
Supplemental information: Additional information regarding the PACRAT system, including sample datasets is available linked from the ‘About’ page of the PACRAT website at: http://www.biosci.ohio-state.edu/~pacrat/.
* To whom correspondence should be addressed.
What are the baselines for protein fold recognition?
Authors: McGuffin Liam J. , Bryson Kevin , Jones David T. 
Published: July 2002

Abstract
Motivation: What constitutes a baseline level of success for protein fold recognition methods? As fold recognition benchmarks are often presented without any thought to the results that might be expected from a purely random set of predictions, an analysis of fold recognition baselines is long overdue. Given varying amounts of basic information about a protein—ranging from the length of the sequence to a knowledge of its secondary structure—to what extent can the fold be determined by intelligent guesswork? Can simple methods that make use of secondary structure information assign folds more accurately than purely random methods and could these methods be used to construct viable hierarchical classifications?
Experiments performed: A number of rapid automatic methods which score similarities between protein domains were devised and tested. These methods ranged from those that incorporated no secondary structure information, such as measuring absolute differences in sequence lengths, to more complex alignments of secondary structure elements. Each method was assessed for accuracy by comparison with the Class Architecture Topology Homology (CATH) classification. Methods were rated against both a random baseline fold assignment method as a lower control and FSSP as an upper control. Similarity trees were constructed in order to evaluate the accuracy of optimum methods at producing a classification of structure.
Results: Using a rigorous comparison of methods with CATH, the random fold assignment method set a lower baseline of 11% true positives allowing for 3% false positives and FSSP set an upper benchmark of 47% true positives at 3% false positives. The optimum secondary structure alignment method used here achieved 27% true positives at 3% false positives. Using a less rigorous Critical Assessment of Structure Prediction (CASP)-like sensitivity measurement the random assignment achieved 6%, FSSP—59% and the optimum secondary structure alignment method—32%. Similarity trees produced by the optimum method illustrate that these methods cannot be used alone to produce a viable protein structural classification system.
Conclusions: Simple methods that use perfect secondary structure information to assign folds cannot produce an accurate protein taxonomy, however they do provide useful baselines for fold recognition. In terms of a typical CASP assessment our results suggest that approximately 6% of targets with folds in the databases could be assigned correctly by randomly guessing, and as many as 32% could be recognised by trivial secondary structure comparison methods, given knowledge of their correct secondary structures.
Contact: David.Jones@brunel.ac.uk
* To whom correspondence should be addressed.
Nucleosome formation potential of exons, introns, and Alu repeats
Authors: Levitsky Victor G. , Podkolodnaya Olga A. , Kolchanov Nikolay A. , Podkolodny Nikolay L. 
Published: July 2002

Abstract
A program for constructing nucleosome formation potential profile was applied for investigation of exons, introns, and repetitive sequences. The program is available at http://wwwmgs.bionet.nsc.ru/mgs/programs/recon/. We have demonstrated that introns and repetitive sequences exhibit higher nucleosome formation potentials than exons. This fact may be explained by functional saturation of exons with genetic code, hindering the localization of efficient nucleosome positioning sites.
Promoter Extraction from GenBank (PEG): automatic extraction of
eukaryotic promoter sequences in large sets of genes
Authors: Zhang Theresa , Zhang Michael 
Published: July 2002

Abstract
Summary: Promoter Extraction from GenBank (PEG) extracts promoter sequences for large sets of genes using information present in GenBank. For a gene whose promoter sequence is not found, PEG will attempt to extract promoter sequences of the orthologous genes instead.
Availability: It is freely available to academic users at ftp://cshl.org/pub/science/mzhanglab/theresa/.
Contact: zhangt@cshl.org; mzhang@cshl.org
* To whom correspondence should be addressed.
Picasso: generating a covering set of protein family profiles
Authors: Heger Andreas , Holm Liisa 
Published: July 2002

Abstract
Motivation: Evolutionary classification leads to an economical description of protein sequence data because attributes of function and structure are inherited in protein families. This paper presents Picasso, a procedure for deriving a minimal set of protein family profiles that cover all known protein sequences.
Results: Picasso starts from highly overlapping sequence neighbourhoods revealed by all-on-all pairwise Blast alignment. Overlaps are reduced by merging sequences or parts of sequences into multiple alignments. For maximum unification, the multiple alignments must reach into the twilight zone of sequence similarity. Sensitive and selective profile–profile comparison allows unification down to about 15% pairwise sequence identity. Families unified through a short conserved sequence motif are associated with multiple full-length alignments describing different subfamilies. Domains that are mobile modules are identified based on their association with different sets of neighbours. The result is 10000 unified domain families (excluding singletons) representing functionally related proteins and recovering classical prolific domain types in high numbers. The classification is useful, for example, in developing strategies for efficient database searching and for selecting targets to complete the map of all 3-D structures.
Availability: http://www.embl-ebi.ac.uk/picasso/picasso.html
Contact: {heger,holm}@embl-ebi.ac.uk
A relational schema for both array-based and SAGE gene

expression experiments
Authors: Stoeckert C. , Pizarro A. , Manduchi E. , Gibson M. , Brunk B. , Crabtree J. , Schug J. , Shen-Orr S. , Overton G. C. 
Published: July 2002

Abstract
Motivation and Results: A relational schema is described for capturing highly parallel gene expression experiments using different technologies. This schema grew out of efforts to build a database for collaborators working on different biological systems and using different types of platforms in their gene expression experiments as well as different types of image quantification software. The tables are conceptually organized into three categories of information: Platform, Experiment (which includes image scanning and quantification), and Data. The strengths of the schema are: (i) integrating information on array elements using a gene index; (ii) describing samples using ontologies; (iii) reducing an experiment to a single RNA source for precise descriptions yet not losing the relationships between experiments done at the same time or for the same project; and (iv) maintaining both raw and processed (e.g. cleansed and normalized) data and recording how the data is processed. The result is a novel schema, which can hold both array and non-array data, is extensible for detailed experimental descriptions that are precise and consistent, and allows for meaningful comparisons of genes between experiments.
Availability: The schema is available at http://www.cbil.upenn.edu/cgi-bin/RAD2/schemaBrowserRAD.pl.
Contact: stoeckrt@pcbi.upenn.edu
* To whom correspondence should be addressed.
2 Present address: Department of Molecular Cell Biology, Weizmann Institute of Science, Israel.
TreeGeneBrowser: phylogenetic data mining of gene sequences
from public databases
Authors: Jakobsen Ingrid B. , Saleeba Jennifer A. , Poidinger Michael , Littlejohn Timothy G. 
Published: July 2002

Abstract
Motivation: Sequence databases represent an enormous resource of phylogenetic information, but there is a lack of tools for accessing that information in order to assess the amount of evolutionary information in these databases that may be suitable for phylogenetic reconstruction and for identifying areas of the taxonomy that are under-represented for specific gene sequences.
Results: We have developed TreeGeneBrowser which allows inspection and evaluation of gene sequence data for phylogenetic reconstruction. This program improves the efficiency of identification of genes that may be useful for particular phylogenetic studies and identifies taxa and taxonomic branches that are under-represented in sequence databases.
Availability: The software described here is available for download from ftp://ftp.angis.org.au/pub/TreeGeneBrowser.
Contact: tim@entigen.com
* To whom correspondence should be addressed.
Visualization of expression clusters using Sammon’s
non-linear mapping
Authors: Ewing Rob M. , Cherry J. Michael 
Published: July 2002

Abstract
Summary: A method of exploratory analysis and visualization of multi-dimensional gene expression data using Sammon’s Non-Linear Mapping (NLM) is presented.
Availability: Scripts are available from the authors.
Contact: ewing@genome.stanford.edu
* To whom correspondence should be addressed.
Physics-based gene identification: proof of concept for
Plasmodium falciparum
Authors: Yeramian Edouard , Bonnefoy Serge , Langsley Gordon 
Published: July 2002

Abstract
The ab initio prediction of new genes in eukaryotic genomes represents a difficult task, notably for the identification of complex split genes. A Physics-Based Gene Identification (PBGI) method was formulated recently (Yeramian, Gene, 255, 139–150, 151–168, 2000a,b) to address this problem, taking as a model the Plasmodium falciparum genome. Here, the predictive power of this method is put under experimental test for this genome. The presented results demonstrate the usefulness of the PBGI as a gene-identification tool for P. falciparum, notably for the discovery of new genes with no homology to known genes. Perspectives opened by this new method for other eukaryotic genomes are also mentioned.
ZTR: a new format for DNA sequence trace data
Authors: Bonfield James K. , Staden Rodger 
Published: July 2002

Abstract
Motivation: To produce an open and extensible file format for DNA trace data which produces compact files suitable for large-scale storage and efficient use of internet bandwidth.
Results: We have created an extensible format named ZTR. For a set of data taken from an ABI-3700 the ZTR format produces trace files which require 61.6% of the disk space used by gzipped SCFv3, and which can be written and read at greater speed. The compression algorithms used for the trace amplitudes are used within the National Center for Biotechnology Information (NCBI) trace archive.
Availability: Source code is available from ftp://ftp.mrc-lmb.cam.ac.uk/pub/staden/io_lib/io_lib.tar.gz. A complete format description can be found at http://www.mrc-lmb.cam.ac.uk/pubseq/ztr.html. Test data is available from ftp://ftp.mrc-lmb.cam.ac.uk/pub/staden/io_lib/test_data.
Contact: jkb@mrc-lmb.cam.ac.uk
* To whom correspondence should be addressed.
Improved database searches for orthologous sequences by
conditioning on outgroup sequences
Authors: Cotter Philip J. , Caffrey Daniel R. , Shields Denis C. 
Published: July 2002

Abstract
Motivation: Searches of biological sequence databases are usually focussed on distinguishing significant from random matches. However, the increasing abundance of related sequences on databases present a second challenge: to distinguish the evolutionarily most closely related sequences (often orthologues) from more distantly related homologues. This is particularly important when searching a database of partial sequences, where short orthologous sequences from a non-conserved region will score much more poorly than non-orthologous (outgroup) sequences from a conserved region.
Results: Such inferences are shown to be improved by conditioning the search results on the scores of an outgroup sequence. The log-odds score for each target sequence identified on the database has the log-odds score of the outgroup sequence subtracted from it. A test group of Caenorhabditis elegans kinase sequences and their identified C.elegans outgroups were searched against a test database of human Expressed Sequence Tag (EST) sequences, where the sets of true target sequences were known in advance. The outgroup conditioned method was shown to identify 58% more true positives ahead of the first false positive, compared to the straightforward search without an outgroup. A test dataset of 151 proteins drawn from the C.elegans genome, where the putative ‘outgroup’ was assigned automatically, similarly found 50% more true positives using outgroup conditioning. Thus, outgroup conditioning provides a means to improve the results of database searching with little increase in the search computation time.
Availability: Perl scripts for the Outgroup Conditioned Score (OCS) method are available without charge for non-profit academic use from http://www.bioinf.org/vibe/software/OCS/. Scripts have been optimized for Linux or OSF with a Perl v5 interpreter.
Contact: dshields@rcsi.ie.
* Non-standard abbreviations: OCS: Outgroup Conditioned Score, HOCS Heuristic Outgroup Conditioned Score, HOCP: Heuristic Outgroup Conditioned P-value ratio, EST: Expressed Sequence Tag.
1 To whom correspondence should be addressed.
Assembly of fingerprint contigs: parallelized FPC
Authors: Ness S. R. , Terpstra W. , Krzywinski M. , Marra M. A. , Jones S. J. M. 
Published: July 2002

Abstract
Summary: One of the more common uses of the program FingerPrint Contigs (FPC) is to assemble random restriction digest ‘fingerprints’ of overlapping genomic clones into contigs. To improve the rate of assembling contigs from large fingerprint databases we have adapted FPC so that it can be run in parallel on multiple processors and servers. The current version of ‘parallelized FPC’ has been used in our laboratory to assemble mammalian BAC fingerprint databases, each containing more than 300000 BAC fingerprints.
Availability: This parallelized version of FPC is available under the GNU GPL licence, and can be downloaded from ftp://ftp.bcgsc.bc.ca/pub/fpcd.
Contact: fpc@bcgsc.bc.ca
* To whom correspondence should be addressed.
Brief communication. High levels of conservation at microsatellite loci among ictalurid catfishes
Authors: Liu Z , Tan G , Kucuktas H , Li P , Karsi A , Yant DR , Dunham RA 
Published: July 2002

Abstract
The potential of microsatellite sequences as genetic markers in channel catfish (Ictalurus punctatus) was investigated with respect to their variability, inheritance, and usefulness in related species. Six small insert genomic DNA libraries enriched for six families of microsatellites of channel catfish were constructed. We describe here the isolation, characterization, and PCR amplification of 32 microsatellites from channel catfish. The flanking primer regions of microsatellite loci were highly conserved between channel catfish and blue catfish (I. furcatus). Of the 32 loci, 29 were amplified from blue catfish using primers designed from channel catfish, indicating conservation of primer binding sequences. Most of the amplified alleles from channel catfish and blue catfish were polymorphic. White catfish (Ameiurus catus) and flathead catfish (Pylodictus olivaris) loci were also amplified. The microsatellite markers are highly polymorphic for all catfish species tested and are inherited as codominant markers. They should be highly useful for construction of genetic linkage maps of catfish and for marker-assisted selection.
Circularly permuted proteins in the protein structure database
Authors: Jung Jongsun , Lee Byungkook 
Published: July 2002

AbstractSome proteins are homologous to others after their sequence is circularly permuted. A few such proteins have been recognized, mainly by sequence comparison, but also by comparing their three‐dimensional structures. Here we report the result of a systematic search for all protein pairs in the SCOP 90% id domain database that become structurally superimposable when the sequence of one of the pairs is circularly permuted. Using a reasonable set of criteria, we find that 47% of all protein domains are superimposable to at least one other protein domain in the database after their sequence is circularly permuted. Many of these are symmetric proteins, which superimpose to another protein both with and without a circular permutation of the sequence. However, 412 of the total 3035 domains are nonsymmetric, and these become structurally superimposable to another protein only after a circular permutation of the sequence. These include most known and many previously undetected circularly permuted proteins with remote homology.
The CATH extended protein‐family database: Providing structural annotations for genome sequences
Authors: Pearl Frances M.G. , Lee David , Bray James E. , Buchan Daniel W.A. , Shepherd Adrian J. , Orengo Christine A. 
Published: July 2002

AbstractAn automatic sequence search and analysis protocol (DomainFinder) based on PSI‐BLAST and IMPALA, and using conservative thresholds, has been developed for reliably integrating gene sequences from GenBank into their respective structural families within the CATH domain database (http://www.biochem.ucl.ac.uk/bsm/cath_new). DomainFinder assigns a new gene sequence to a CATH homologous superfamily provided that PSI‐BLAST identifies a clear relationship to at least one other Protein Data Bank sequence within that superfamily. This has resulted in an expansion of the CATH protein family database (CATH‐PFDB v1.6) from 19,563 domain structures to 176,597 domain sequences. A further 50,000 putative homologous relationships can be identified using less stringent cut‐offs and these relationships are maintained within neighbour tables in the CATH Oracle database, pending further evidence of their suggested evolutionary relationship. Analysis of the CATH‐PFDB has shown that only 15% of the sequence families are close enough to a known structure for reliable homology modeling. IMPALA/PSI‐BLAST profiles have been generated for each of the sequence families in the expanded CATH‐PFDB and a web server has been provided so that new sequences may be scanned against the profile library and be assigned to a structure and homologous superfamily.