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Nucleic Acids Res. 2008 Jan;36(Database issue):D263-6. Epub 2007 Nov 30.

InParanoid 6: eukaryotic ortholog clusters with inparalogs.

Author information

1
Linnaeus Centre for Bioinformatics, Uppsala University, BMC Box 598, 75124, Uppsala, Sweden.

Abstract

The InParanoid eukaryotic ortholog database (http://InParanoid.sbc.su.se/) has been updated to version 6 and is now based on 35 species. We collected all available 'complete' eukaryotic proteomes and Escherichia coli, and calculated ortholog groups for all 595 species pairs using the InParanoid program. This resulted in 2 642 187 pairwise ortholog groups in total. The orthology-based species relations are presented in an orthophylogram. InParanoid clusters contain one or more orthologs from each of the two species. Multiple orthologs in the same species, i.e. inparalogs, result from gene duplications after the species divergence. A new InParanoid website has been developed which is optimized for speed both for users and for updating the system. The XML output format has been improved for efficient processing of the InParanoid ortholog clusters.

PMID:
18055500
PMCID:
PMC2238924
DOI:
10.1093/nar/gkm1020
[Indexed for MEDLINE]
Free PMC Article

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