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Database Commons - GreenPhylDB

GreenPhylDB

Citations: 130

z-index 2.60

Short name GreenPhylDB
Full name GreenPhylDB
Description GreenPhylDB is a web resource designed for comparative and functional genomics in plants. The database contains a catalogue of gene families based on gene predictions of genomes, covering a broad taxonomy of green plants.
URL http://greenphyl.cirad.fr/
Year founded 2007
Last update & version 2015-09-04    v4.0
Availability Free to all users
University/Institution hosted Bioversity International - CfL programme Parc Scientifique Agropolis II
Address 34397 Montpellier,France
City Montpellier
Province/State
Country/Region France
Contact name Mathieu Rouard
Contact email m.rouard@cgiar.org
Data type(s)
Major organism(s)
Keyword(s)
  • comparative genomics
  • functional genomics
Publication(s)
  • GreenPhylDB v2.0: comparative and functional genomics in plants. [PMID: 20864446]

    Mathieu Rouard, Valentin Guignon, Christelle Aluome, Marie-Angélique Laporte, Gaëtan Droc, Christian Walde, Christian M Zmasek, Christophe Périn, Matthieu G Conte
    Nucleic acids research 2011:39(Database issue)
    71 Citations (Google Scholar as of 2016-06-09)

    Abstract: GreenPhylDB is a database designed for comparative and functional genomics based on complete genomes. Version 2 now contains sixteen full genomes of members of the plantae kingdom, ranging from algae to angiosperms, automatically clustered into gene families. Gene families are manually annotated and then analyzed phylogenetically in order to elucidate orthologous and paralogous relationships. The database offers various lists of gene families including plant, phylum and species specific gene families. For each gene cluster or gene family, easy access to gene composition, protein domains, publications, external links and orthologous gene predictions is provided. Web interfaces have been further developed to improve the navigation through information related to gene families. New analysis tools are also available, such as a gene family ontology browser that facilitates exploration. GreenPhylDB is a component of the South Green Bioinformatics Platform (http://southgreen.cirad.fr/) and is accessible at http://greenphyl.cirad.fr. It enables comparative genomics in a broad taxonomy context to enhance the understanding of evolutionary processes and thus tends to speed up gene discovery.

  • GreenPhylDB: a database for plant comparative genomics. [PMID: 17986457]

    M G Conte, S Gaillard, N Lanau, M Rouard, C Périn
    Nucleic acids research 2008:36(Database issue)
    59 Citations (Google Scholar as of 2016-06-09)

    Abstract: 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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Tags

DNA Expression RNA
Plant
comparative genomics functional genomics

Record metadata

  • Created on: 2015-06-20
  • Curated by:
    • Lin Liu [2016-03-26]
    • Jian Sang [2015-12-05]
    • Jian Sang [2015-06-28]
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