New release of the InParanoid ortholog database

Published: 2014-01-28


A new version of the InParanoid ortholog database, developed at SciLifeLab and Bioinformatics Infrastructure for Life Sciences (BILS), has been released online.

Orthologs are genes in different species that derive from the same gene in their last common ancestor. Because of this, orthologs are likely to have the same function.  This makes them ideal to predict gene function, by transferring known functional annotations­ from orthologs in model organisms. Sometimes an ortholog is duplicated after the speciation event that separated them. Such copied orthologs are called inparalogs and they are needed to obtain the complete evolutionary picture. The presence of multiple inparalogs also has major implications on experimental design and interpretation.

To he specifically to find inparalogs, InParanoid algorithm was developed, which is used in the InParanoid database. Recently a new version of the database, InParanoid 8.0, was released. It contains orthologs between 273 species – 246 eukaryotes, 20 bacteria, and 7 archaea. In total 3,718,323 gene sequences were processed to obtain the database. Compared to the previous release the number of species is increased by 173%, the number of species pairs by 650%, and the number of genes by 120%.  Previously, InParanoid was based on eukaryotes only, but in the new release a number of prokaryotes are included thanks to the Quest for Orthologs Reference Proteomes. The InParanoid databse has 20 000 visits per year.

“The increased species coverage of InParanoid 8 substantially improves its usefulness for researchers in comparative genomics”, says Erik Sonnhammer, Professor of Bioinformatics at Stockholm University/SciLifeLab who is one of the researchers behind the database.

Release 8 was produced mainly by Dr. Gabriel Östlund with a grant from BILS.