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Nucleic Acids Research 2005 33(Database Issue):D476-D480; doi:10.1093/nar/gki107
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Nucleic Acids Research, 2005, Vol. 33, Database issue D476-D480
© 2005, the authors
Nucleic Acids Research, Vol. 33, Database issue © Oxford University Press 2005; all rights reserved

Inparanoid: a comprehensive database of eukaryotic orthologs

Kevin P. O'Brien, Maido Remm1 and Erik L. L. Sonnhammer*

Center for Genomics and Bioinformatics, Karolinska Institutet, S-171 77 Stockholm, Sweden and 1 Estonian Biocentre and Department of Bioinformatics, Institute of Molecular and Cell Biology, University of Tartu, Estonia

* To whom correspondence should be addressed. Tel: +46 8 52486395; Fax: +46 8 337983; Email: Erik.Sonnhammer{at}cgb.ki.se

Recieved August 15, 2004; Revised and Accepted October 18, 2004

The Inparanoid eukaryotic ortholog database (http://inparanoid.cgb.ki.se/) is a collection of pairwise ortholog groups between 17 whole genomes; Anopheles gambiae, Caenorhabditis briggsae, Caenorhabditis elegans, Drosophila melanogaster, Danio rerio, Takifugu rubripes, Gallus gallus, Homo sapiens, Mus musculus, Pan troglodytes, Rattus norvegicus, Oryza sativa, Plasmodium falciparum, Arabidopsis thaliana, Escherichia coli, Saccharomyces cerevisiae and Schizosaccharomyces pombe. Complete proteomes for these genomes were derived from Ensembl and UniProt and compared pairwise using Blast, followed by a clustering step using the Inparanoid program. An Inparanoid cluster is seeded by a reciprocally best-matching ortholog pair, around which inparalogs (should they exist) are gathered independently, while outparalogs are excluded. The ortholog clusters can be searched on the website using Ensembl gene/protein or UniProt identifiers, annotation text or by Blast alignment against our protein datasets. The entire dataset can be downloaded, as can the Inparanoid program itself.

The online version of this article has been published under an open access model. Users are entitled to use, reproduce, disseminate, or display the open access version of this article for non-commercial purposes provided that: the original authorship is properly and fully attributed; the Journal and Oxford University Press are attributed as the original place of publication with the correct citation details given; if an article is subsequently reproduced or disseminated not in its entirety but only in part or as a derivative work this must be clearly indicated. For commercial re-use permissions, please contact journals.permissions{at}oupjournals.org.


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