GreenPhylDB -- a database for plant comparative genomics
What you can do:
A comprehensive platform designed to facilitate comparative functional genomics in Oryza sativa and Arabidopsis thaliana genomes.
Highlights:
- 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.
- 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.
Keywords:
- Oryza sativa
- Oryza
- Arabidopsis thaliana
- Arabidopsis
- rice
- plant protein
- comparative plant genomics
- phylogenomic
Literature & Tutorials:
This record last updated: 04-17-2014