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Journal Articles Bioinformatics Year : 2005

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

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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.

Dates and versions

ensl-00175665 , version 1 (29-09-2007)

Identifiers

Cite

Leon Goldovsky, Paul Janssen, Dag Ahrén, Benjamin Audit, Ildefonso Cases, et al.. CoGenT++: an extensive and extensible data environment for computational genomics.. Bioinformatics, 2005, 19 (21), pp.3806-10. ⟨10.1093/bioinformatics/bti579⟩. ⟨ensl-00175665⟩
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