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Nucleic Acids Research Advance Access originally published online on November 5, 2007
Nucleic Acids Research 2008 36(Database issue):D255-D262; doi:10.1093/nar/gkm924
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Nucleic Acids Research, 2008, Vol. 36, Database issue D255-D262
© 2007 The Author(s)
This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/2.0/uk/) which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.

This article appears in the following Nucleic Acids Research issue: Database issue [View the issue table of contents]

Articles

EPGD: a comprehensive web resource for integrating and displaying eukaryotic paralog/paralogon information

Guohui Ding1,2, Yan Sun1,2, Hong Li1,2, Zhen Wang1,2, Haiwei Fan1, Chuan Wang1, Dan Yang4 and Yixue Li1,3,*

1Bioinformatics Center, Key Lab of Systems Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, 320 Yueyang Road, 2Graduate School of the Chinese Academy of Sciences, Shanghai 200031, 3Shanghai Center for Bioinformation Technology, 100 Qinzhou Road, Shanghai 200235 and 4Shanghai Information Center for Life Sciences, Shanghai Institutes for Biology Science, Chinese Academy of Science, Shanghai 200031, P. R. China

*To whom correspondence should be addressed. Tel: +86 21 54920089; Fax: +86 21 54920143; Email: yxli{at}sibs.ac.cn

Received August 4, 2007. Revised October 8, 2007. Accepted October 10, 2007.

Gene duplication is common in all three domains of life, especially in eukaryotic genomes. The duplicates provide new material for the action of evolutionary forces such as selection or genetic drift. Here we describe a sophisticated procedure to extract duplicated genes (paralogs) from 26 available eukaryotic genomes, to pre-calculate several evolutionary indexes (evolutionary rate, synonymous distance/clock, transition redundant exchange clock, etc.) based on the paralog family, and to identify block or segmental duplications (paralogons). We also constructed an internet-accessible Eukaryotic Paralog Group Database (EPGD; http://epgd.biosino.org/EPGD/). The database is gene-centered and organized by paralog family. It focuses on paralogs and evolutionary duplication events. The paralog families and paralogons can be searched by text or sequence, and are downloadable from the website as plain text files. The database will be very useful for both experimentalists and bioinformaticians interested in the study of duplication events or paralog families.

The authors wish it to be known that, in their opinion, the first two authors should be regarded as joint First Authors.


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