InParanoid 6:: eukaryotic ortholog clusters with inparalogs

被引：173

作者：

Berglund, Ann-Charlotte ^{[2
]}

Sjolund, Erik ^{[1
]}

Ostlund, Gabriel ^{[1
]}

Sonnhammer, Erik L. L. ^{[1
]}

机构：

[1] Stockholm Univ, Stockholm Bioinformat Ctr, SE-10691 Stockholm, Sweden

[2] Uppsala Univ, Linnaeus Ctr Bioinformat, S-75124 Uppsala, Sweden

来源：

NUCLEIC ACIDS RESEARCH | 2008年 / 36卷

关键词：

D O I：

10.1093/nar/gkm1020

中图分类号：

Q5 [生物化学]; Q7 [分子生物学];

学科分类号：

071010 ; 081704 ;

摘要：

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.

引用

页码：D263 / D266

页数：4

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