Nucleic Acids Research Advance Access originally published online on November 30, 2007
Nucleic Acids Research 2008 36(Database issue):D263-D266; doi:10.1093/nar/gkm1020
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Nucleic Acids Research, 2008, Vol. 36, Database issue D263-D266
© 2007 The Author(s)
This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/2.0/uk/) which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.
This article appears in the following Nucleic Acids Research issue: Database issue [View the issue table of contents]
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InParanoid 6: eukaryotic ortholog clusters with inparalogs
1Linnaeus Centre for Bioinformatics, Uppsala University, BMC Box 598, 75124, Uppsala and 2Stockholm Bioinformatics Center, Albanova, Stockholm University, SE-10691 Stockholm, Sweden
*To whom correspondence should be addressed. Tel: +46 8 55378567; Fax: +46 8 55378214; Email: Erik.Sonnhammer{at}sbc.su.se
Received September 15, 2007. Revised October 23, 2007. Accepted October 27, 2007.
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.
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