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GreenPhylDB: a database for plant comparative genomics.

M G Conte1, S Gaillard, N Lanau

  • 1CIRAD, Department BIOS, UMR DAP-TA40/03, 34398 Montpellier, France.

Nucleic Acids Research
|November 8, 2007
PubMed
Summary
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GreenPhylDB offers a comprehensive resource for plant comparative genomics, enabling gene family assignment and ortholog group creation for rice and Arabidopsis. This platform aids in understanding plant gene function and evolutionary relationships.

Area of Science:

  • Plant genomics
  • Bioinformatics
  • Comparative genomics

Background:

  • Comparative functional genomics requires robust tools for analyzing plant genomes.
  • Databases integrating gene families and orthologous relationships are crucial for research.

Purpose of the Study:

  • To present GreenPhylDB, a platform for comparative functional genomics in *Oryza sativa* (rice) and *Arabidopsis thaliana*.
  • To facilitate gene family assignment and the creation of orthologous groups using phylogenomic approaches.

Main Methods:

  • Semi-automatic clustering procedures for gene family assignment.
  • Phylogenomic approaches to define orthologous groups.
  • Integration of data from UniProt, KEGG, InterPro, TAIR, and TIGR databases.

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Main Results:

  • GreenPhylDB contains 6421 manually curated plant gene families.
  • Phylogenomic relationships for 4375 families are computed and available.
  • Manual curation involved 492 TAIR, 1903 InterPro, and 981 KEGG families/subfamilies.
  • The GreenPhyl Ortholog Search Tool (GOST) enables ortholog prediction across plant species.

Conclusions:

  • GreenPhylDB provides a valuable, manually curated resource for plant gene family and ortholog analysis.
  • The platform enhances comparative genomics research by integrating diverse data and offering powerful search tools.