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

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.
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Submitted on : Saturday, September 29, 2007 - 2:29:41 PM
Last modification on : Monday, November 29, 2021 - 1:10:04 PM

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



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