Dear all,
Could you suggest me some good plant orthologous gene databases? I search biostar, but have not found plant ortho-db. To my knowledge Ensembl collected many plant species, but I would like to know others, one reason is the Ensembl rice cds db does not have as many sequences as MSU rice db does. Your suggestions will be much appreciated. THANKS.
There is the GreenPhylDB
Rouard M, Guignon V, Aluome C, Laporte MA, Droc G, Walde C, Zmasek CM, Périn C, Conte MG: GreenPhylDB v2.0: comparative and functional genomics in plants. Nucleic Acids Res 2011, 39: D1095-D1102.
The relationship between the sequences are computed by clustering. Keep in mind that they first create clusters, then build one phylogeny by cluster.
reviving an old thread, but if you are interested in these kind of questions/data you should get a look at PLAZA , frequently updated and holds much more species than most other similar resources.
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Hi Juke, thanks a lot. Your comments are really helpful!
You can also generate orthologs by best reciprocal blast.