InParanoid 8: orthology analysis between 273 proteomes, mostly eukaryotic

Erik L L Sonnhammer; Gabriel Östlund

doi:10.1093/nar/gku1203

InParanoid 8: orthology analysis between 273 proteomes, mostly eukaryotic

Nucleic Acids Res. 2015 Jan;43(Database issue):D234-9. doi: 10.1093/nar/gku1203. Epub 2014 Nov 27.

Authors

Erik L L Sonnhammer¹, Gabriel Östlund²

Affiliations

¹ Stockholm Bioinformatics Center, Department of Biochemistry and Biophysics, Stockholm University, Science for Life Laboratory, Box 1031, SE-17121 Solna, Sweden erik.sonnhammer@scilifelab.se.
² Stockholm Bioinformatics Center, Department of Biochemistry and Biophysics, Stockholm University, Science for Life Laboratory, Box 1031, SE-17121 Solna, Sweden.

Abstract

The InParanoid database (http://InParanoid.sbc.su.se) provides a user interface to orthologs inferred by the InParanoid algorithm. As there are now international efforts to curate and standardize complete proteomes, we have switched to using these resources rather than gathering and curating the proteomes ourselves. InParanoid release 8 is based on the 66 reference proteomes that the 'Quest for Orthologs' community has agreed on using, plus 207 additional proteomes from the UniProt complete proteomes--in total 273 species. These represent 246 eukaryotes, 20 bacteria and seven archaea. Compared to the previous release, this increases the number of species by 173% and the number of pairwise species comparisons by 650%. In turn, the number of ortholog groups has increased by 423%. We present the contents and usages of InParanoid 8, and a detailed analysis of how the proteome content has changed since the previous release.

Publication types

Research Support, Non-U.S. Gov't

MeSH terms

Algorithms
Databases, Protein*
Proteome / chemistry*
Sequence Homology, Amino Acid*

Substances

Proteome