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Bioinformatics 2005 21(19):3806-3810; doi:10.1093/bioinformatics/bti579
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© The Author 2005. Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions{at}oxfordjournals.org

CoGenT++: an extensive and extensible data environment for computational genomics

Leon Goldovsky 1, Paul Janssen 2, Dag Ahrén 1,3, Benjamin Audit 4, Ildefonso Cases 5, Nikos Darzentas 1, Anton J. Enright 6, Núria López-Bigas 1, José M. Peregrin-Alvarez 7, Mike Smith 1, Sophia Tsoka 1, Victor Kunin 1,8 and Christos A. Ouzounis 1,*

1Computational Genomics Group, The European Bioinformatics Institute EMBL, Cambridge Outstation, Cambridge CB10 1SD, UK
2Laboratory for Microbiology, Belgian Nuclear Research Center SCK/CEN, Boeretang 200, Mol B-2400, Belgium
3Institute of Agrobiotechnology, National Center for Research and Technology PO Box 361, Thermi, Thessaloniki GR-57001, Greece
4Laboratoire de Physique, Ecole Normale Supérieure 46 Allée d' Italie, Lyon CEDEX 07 F-69364, France
5Transcription Networks Group, National Center for Biotechnology CNB-CSIC Cantoblanco, Madrid E-28049, Spain
6Sanger Institute Wellcome Trust Campus, Cambridge CB10 1SA, UK
7Hospital for Sick Children, 555 University Avenue Toronto, Canada, ON M5G 1X
8DOE Joint Genome Institute 2800 Mitchell Drive, Walnut Creek, CA 94598, USA

*To whom correspondence should be addressed.

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{at}ebi.ac.uk

Received on April 6, 2005; revised on July 5, 2005; accepted on July 6, 2005

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