Question: Plant orthologous gene database
1
gravatar for biolab
3.2 years ago by
biolab970
biolab970 wrote:

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.

orthologous database • 1.7k views
ADD COMMENTlink modified 3.2 years ago by Juke-341.1k • written 3.2 years ago by biolab970
2
gravatar for Juke-34
3.2 years ago by
Juke-341.1k
Sweden
Juke-341.1k wrote:

There is the GreenPhylDB => http://www.greenphyl.org/cgi-bin/index.cgi 

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.

ADD COMMENTlink written 3.2 years ago by Juke-341.1k

Hi Juke, thanks a lot. Your comments are really helpful!

ADD REPLYlink written 3.2 years ago by biolab970

You can also generate orthologs by best reciprocal blast.

ADD REPLYlink written 3.2 years ago by pld4.6k
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