CoGenT++: an extensive and extensible data environment for computational genomics
Identifieur interne : 000184 ( France/Analysis ); précédent : 000183; suivant : 000185CoGenT++: an extensive and extensible data environment for computational genomics
Auteurs : Leon Goldovsky [Royaume-Uni] ; Paul Janssen [Belgique] ; Dag Ahre N [Royaume-Uni, Grèce] ; Benjamin Audit [France] ; Ildefonso Cases [Espagne] ; Nikos Darzentas [Royaume-Uni] ; Anton J. Enright [Royaume-Uni] ; Nu Ria Lo Pez-Bigas [Royaume-Uni] ; Jose M. Peregrin-Alvarez ; Mike Smith [Royaume-Uni] ; Sophia Tsoka [Royaume-Uni] ; Victor Kunin [Royaume-Uni, États-Unis] ; Christos A. Ouzounis [Royaume-Uni]Source :
- Bioinformatics [ 1367-4803 ] ; 2005-01.
Abstract
Motivation: CoGenT++ is a data environment for computational research in comparative and functional genomics, designed to address issues of consistency, reproducibility, scalability and accessibility. Description: CoGenT++ facilitates the re-distribution of all fully sequenced and published genomes, storing information about species, gene names and protein sequences. We describe our scalable implementation of ProXSim, a continually updated all-against-all similarity database, which stores pairwise relationships between all genome sequences. Based on these similarities, derived databases are generated for gene fusions—AllFuse, putative orthologs—OFAM, protein families—TRIBES, phylogenetic profiles—ProfUse and phylogenetic trees. Extensions based on the CoGenT++ environment include disease gene prediction, pattern discovery, automated domain detection, genome annotation and ancestral reconstruction. Conclusion: CoGenT++ provides a comprehensive environment for computational genomics, accessible primarily for large-scale analyses as well as manual browsing. Availability: The database and component downloads are accessible at http://cgg.ebi.ac.uk/cogentpp.html. Contact: ouzounis@ebi.ac.uk
Url:
DOI: 10.1093/bioinformatics/bti579
Affiliations:
- Belgique, Espagne, France, Grèce, Royaume-Uni, États-Unis
- Auvergne-Rhône-Alpes, Californie, Communauté de Madrid, Rhône-Alpes
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ISTEX:F79304AC78B17B494B843AFC3BBEF28E3FF872E2Le document en format XML
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Ouzounis</name><affiliation wicri:level="1"><country xml:lang="fr">Royaume-Uni</country><wicri:regionArea>Computational Genomics Group, The European Bioinformatics Institute EMBL, Cambridge Outstation, Cambridge CB10 1SD</wicri:regionArea><wicri:noRegion>Cambridge CB10 1SD</wicri:noRegion></affiliation><affiliation></affiliation></author></analytic><monogr></monogr><series><title level="j">Bioinformatics</title><title level="j" type="abbrev">Bioinformatics</title><idno type="ISSN">1367-4803</idno><idno type="eISSN">1460-2059</idno><imprint><publisher>Oxford University Press</publisher><date type="published" when="2005-01">2005-01</date><biblScope unit="volume">21</biblScope><biblScope unit="issue">19</biblScope><biblScope unit="page" from="3806">3806</biblScope><biblScope unit="page" to="3810">3810</biblScope></imprint><idno type="ISSN">1367-4803</idno></series><idno type="istex">F79304AC78B17B494B843AFC3BBEF28E3FF872E2</idno><idno type="DOI">10.1093/bioinformatics/bti579</idno><idno type="local">bti579</idno></biblStruct></sourceDesc><seriesStmt><idno type="ISSN">1367-4803</idno></seriesStmt></fileDesc><profileDesc><textClass></textClass><langUsage><language ident="en">en</language></langUsage></profileDesc></teiHeader><front><div type="abstract" xml:lang="en">Motivation: CoGenT++ is a data environment for computational research in comparative and functional genomics, designed to address issues of consistency, reproducibility, scalability and accessibility. Description: CoGenT++ facilitates the re-distribution of all fully sequenced and published genomes, storing information about species, gene names and protein sequences. We describe our scalable implementation of ProXSim, a continually updated all-against-all similarity database, which stores pairwise relationships between all genome sequences. Based on these similarities, derived databases are generated for gene fusions—AllFuse, putative orthologs—OFAM, protein families—TRIBES, phylogenetic profiles—ProfUse and phylogenetic trees. Extensions based on the CoGenT++ environment include disease gene prediction, pattern discovery, automated domain detection, genome annotation and ancestral reconstruction. Conclusion: CoGenT++ provides a comprehensive environment for computational genomics, accessible primarily for large-scale analyses as well as manual browsing. Availability: The database and component downloads are accessible at http://cgg.ebi.ac.uk/cogentpp.html. Contact: ouzounis@ebi.ac.uk</div></front></TEI><affiliations><list><country><li>Belgique</li><li>Espagne</li><li>France</li><li>Grèce</li><li>Royaume-Uni</li><li>États-Unis</li></country><region><li>Auvergne-Rhône-Alpes</li><li>Californie</li><li>Communauté de Madrid</li><li>Rhône-Alpes</li></region></list><tree><noCountry><name sortKey="Peregrin Alvarez, Jose M" sort="Peregrin Alvarez, Jose M" uniqKey="Peregrin Alvarez J" first="Jose M." last="Peregrin-Alvarez">Jose M. 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Ouzounis</name><name sortKey="Smith, Mike" sort="Smith, Mike" uniqKey="Smith M" first="Mike" last="Smith">Mike Smith</name><name sortKey="Tsoka, Sophia" sort="Tsoka, Sophia" uniqKey="Tsoka S" first="Sophia" last="Tsoka">Sophia Tsoka</name></country><country name="Belgique"><noRegion><name sortKey="Janssen, Paul" sort="Janssen, Paul" uniqKey="Janssen P" first="Paul" last="Janssen">Paul Janssen</name></noRegion></country><country name="Grèce"><noRegion><name sortKey="Ahre N, Dag" sort="Ahre N, Dag" uniqKey="Ahre N D" first="Dag" last="Ahre N">Dag Ahre N</name></noRegion></country><country name="France"><region name="Auvergne-Rhône-Alpes"><name sortKey="Audit, Benjamin" sort="Audit, Benjamin" uniqKey="Audit B" first="Benjamin" last="Audit">Benjamin Audit</name></region></country><country name="Espagne"><region name="Communauté de Madrid"><name sortKey="Cases, Ildefonso" sort="Cases, Ildefonso" uniqKey="Cases I" first="Ildefonso" last="Cases">Ildefonso Cases</name></region></country><country name="États-Unis"><region name="Californie"><name sortKey="Kunin, Victor" sort="Kunin, Victor" uniqKey="Kunin V" first="Victor" last="Kunin">Victor Kunin</name></region></country></tree></affiliations></record>Pour manipuler ce document sous Unix (Dilib)
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