GreenPhylDB: a database for plant comparative genomics

Proprietary Rights Notice for Nucleic Acids Research Online 1. The person using Nucleic Acids Research Online may use, reproduce, disseminate, or display the open access version of content from this journal for non-commercial purposes 2. ANY USE of the open access version of this Journal in whole or in part must include the customary bibliographic citation, including author and publisher attribution, date, article title, Nucleic Acids Research, and the URL http://nar.oxfordjournals.org/ and MUST include a copy of the copyright notice. If an original work is subsequently reproduced or disseminated not in its entirety but only in part or as a derivative work this must be clearly indicated 3. For any commercial use of material from the open access version of the journal, permission MUST be obtained from Oxford University Press. Email: journals.permissions@oxfordjournals.org 4. Commercial use is defined as being ANY kind of re-use for the commercial gain of the user, their employing institution and/or any other third party. Examples of commercial use include: 1. re-use by a non-author/third party/other publisher of parts of or all of an article or articles in another publication (journal or book) to be sold for commercial purposes 2. the proactive supply of multiple print or electronic copies of items taken from the Journal to third parties on a systematic basis for marketing purposes 3. re-use by an author of parts of or all of an article in other publications from commercial organizationsInternational audienceGreenPhylDB (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 specie