Nucleic Acids Research Advance Access originally published online on November 5, 2007
Nucleic Acids Research 2008 36(Database issue):D991-D998; doi:10.1093/nar/gkm934
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Nucleic Acids Research, 2008, Vol. 36, Database issue D991-D998
© 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 |
GreenPhylDB: a database for plant comparative genomics
1CIRAD, Department BIOS, UMR DAP - TA40/03, 34398 Montpellier, 2INRA UMR Génétique et Horticulture (GenHort) - BP 60057 - 49071 Beaucouzé cedex and 3Bioversity International - Commodites for livelihood programme Parc Scientifique Agropolis II, 34397 Montpellier - Cedex 5, France
*To whom correspondence should be addressed. Tel: +33 0 4 67 61 71 85; Fax: +33 0 4 67 61 56 05; Email: perin{at}cirad.fr
Received August 14, 2007. Revised October 9, 2007. Accepted October 11, 2007.
GreenPhylDB (http://greenphyl.cirad.fr) is a comprehensive platform designed to facilitate comparative functional genomics in Oryza sativa and Arabidopsis thaliana genomes. The main functions of GreenPhylDB are to assign O. sativa and A. thaliana sequences to gene families using a semi-automatic clustering procedure and to create ‘orthologous’ groups using a phylogenomic approach. To date, GreenPhylDB comprises the most complete list of plant gene families, which have been manually curated (6421 families). GreenPhylDB also contains all of the phylogenomic relationships computed for 4375 families. A total of 492 TAIR, 1903 InterPro and 981 KEGG families and subfamilies were manually curated using the clusters created with the TribeMCL software. GreenPhylDB integrates information from several other databases including UniProt, KEGG, InterPro, TAIR and TIGR. Several entry points can be used to display phylogenomic relationships for A. thaliana or O. sativa sequences, using TAIR, TIGR gene ID, family name, InterPro, gene alias, UniProt or protein/nucleic sequence. Finally, a powerful phylogenomics tool, GreenPhyl Ortholog Search Tool (GOST), was incorporated into GreenPhylDB to predict orthologous relationships between O. sativa/A. thaliana protein(s) and sequences from other plant species.
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