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InParanoid 6: eukaryotic ortholog clusters with inparalogs - PubMed

  • ️Tue Nov 10 2105

. 2008 Jan;36(Database issue):D263-6.

doi: 10.1093/nar/gkm1020. Epub 2007 Nov 30.

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InParanoid 6: eukaryotic ortholog clusters with inparalogs

Ann-Charlotte Berglund et al. Nucleic Acids Res. 2008 Jan.

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.

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Figures

Figure 1.
Figure 1.

Orthophylogram of all 35 species in InParanoid 6. This UPGMA tree is based on the average fraction of orthologs between species. For instance, on average 91.2% of the proteins in H. sapiens and P. troglodytes are orthologous. The tree topology generally corresponds to the standard taxonomy, but a few exceptions were noted (see text).

Figure 2.
Figure 2.

Histogram of average number of inparalogs/cluster per species for all species–species comparisons in InParanoid 6. The peak around five inparalogs/cluster is entirely caused by O. sativa, rice.

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