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InParanoid 8: orthology analysis between 273 proteomes, mostly eukaryotic
Stockholm University, Faculty of Science, Department of Biochemistry and Biophysics. Stockholm University, Science for Life Laboratory (SciLifeLab).
Stockholm University, Faculty of Science, Department of Biochemistry and Biophysics. Stockholm University, Science for Life Laboratory (SciLifeLab).
2015 (English)In: Nucleic Acids Research, ISSN 0305-1048, E-ISSN 1362-4962, Vol. 43, no D1, D234-D239 p.Article in journal (Refereed) Published
Abstract [en]

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.

Place, publisher, year, edition, pages
2015. Vol. 43, no D1, D234-D239 p.
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Biochemistry and Molecular Biology
Identifiers
URN: urn:nbn:se:su:diva-116555DOI: 10.1093/nar/gku1203ISI: 000350210400037PubMedID: 25429972OAI: oai:DiVA.org:su-116555DiVA: diva2:807650
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AuthorCount:2;

Available from: 2015-04-24 Created: 2015-04-21 Last updated: 2017-12-04Bibliographically approved

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