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InParanoid 8: orthology analysis between 273 proteomes, mostly eukaryotic
Erik L L Sonnhammer1, Gabriel Östlund2
1Stockholm Bioinformatics Center, Department of Biochemistry and Biophysics, Stockholm University, Science for Life Laboratory, Box 1031, SE-17121 Solna, Sweden erik.sonnhammer@scilifelab.se.
Nucleic Acids Research
|November 29, 2014
Summary
The InParanoid database now offers a vastly expanded collection of ortholog groups, incorporating 273 species from standardized proteomes. This significant update enhances comparative genomics research by providing more comprehensive evolutionary insights.
Area of Science:
- Comparative genomics
- Bioinformatics
- Evolutionary biology
Background:
- The InParanoid database facilitates access to orthologs identified via the InParanoid algorithm.
- Standardization efforts in complete proteome curation are advancing internationally.
Purpose of the Study:
- To present the contents and usage of InParanoid release 8.
- To detail changes in proteome content compared to previous releases.
- To leverage standardized proteomes for ortholog inference.
Main Methods:
- Utilized 66 reference proteomes from the 'Quest for Orthologs' community.
- Integrated 207 additional proteomes from UniProt's complete proteomes dataset.
- Applied the InParanoid algorithm for ortholog inference across 273 species.
Main Results:
- InParanoid release 8 includes 273 species (246 eukaryotes, 20 bacteria, 7 archaea).
- Represents a 173% increase in species and a 650% increase in pairwise comparisons over the previous release.
- Observed a 423% increase in the number of ortholog groups.
Conclusions:
- InParanoid release 8 offers a significantly expanded resource for ortholog data.
- The adoption of standardized proteomes enhances the database's scope and reliability.
- The updated database supports more robust evolutionary and comparative genomic analyses.
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