Inparanoid program was developed at the Center for Genomics and Bioinformatics to address the need to identify orthologs. Homologs that originate from a speciation event are called orthologs and homologs that originate from a gene duplication event are called paralogs. If a duplication event predates the speciation event the parlogs are called outparalogs, and they can be present in different species. If instead an ortholog undegoes one or several duplication events, the resulting paralogs are called inparalogs, and they are co-orthologs to one or more orthologs in another species. Since an outparalog pair ought to have a more diversified function than inparalogs, it is useful to distinguish between the two. Furthermore, clustering inparalogs together allows proper identification of both one-to-one and many-to-many orthology cases.
InParanoid Version 4.1 is available – email inparanoid@ sbc.su.se to obtain a copy.
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“InParanoid 6: eukaryotic ortholog clusters with inparalogs”
Berglund AC, Sjolund E, Ostlund G, Sonnhammer ELL
Nucleic Acids Res. 36:D263-266 (2008) [PDF]
“Inparanoid: A Comprehensive Database of Eukaryotic Orthologs”
O’Brien Kevin P, Remm Maido and Sonnhammer Erik L.L
NAR 33:D476-D480 (2005) [PDF]
“Automatic clustering of orthologs and in-paralogs from pairwise species comparisons”
Maido Remm, Christian E. V. Storm, and Erik L. L. Sonnhammer
J. Mol. Biol. 314:1041-1052 (2001) [PDF]