Question: OMA - How to retrieve orthologs of only one representative of each taxonomy rank?
0
gravatar for anusblat
14 months ago by
anusblat0
anusblat0 wrote:

Hello everybody? I want to retrieve the ortholog sequences of only one representative of each taxonomy rank (for expample phylum). For example: I have 338 orthologs of the Entry ASPTN10103 (Q0CIE2). I want to download only one (or two or three) representative of any different Phylum. Any one knows if this can be done? and how?

Kind regards, Thank you,

Alejandro

oma orthologs oma orthologs • 369 views
ADD COMMENTlink modified 14 months ago by Christophe Dessimoz590 • written 14 months ago by anusblat0
1
gravatar for Christophe Dessimoz
14 months ago by
University College London
Christophe Dessimoz590 wrote:

You can use the REST API (https://omabrowser.org/api/docs), or if you are using R you could use our bioconductor package OmaDb (https://bioconductor.org/packages/release/bioc/html/OmaDB.html).

Either way, you could retrieve the taxonomy tree of all species in OMA (e.g. GET /api/taxonomy/?type=newick), retrieve the list of orthologs for your entry (GET /api/protein/ASPTN10103/orthologs/) and keep at most 1, 2 or 3 orthologs per phylum.

ADD COMMENTlink written 14 months ago by Christophe Dessimoz590
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