Question: OMA - How to retrieve orthologs of only one representative of each taxonomy rank?
0
gravatar for anusblat
4 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 • 186 views
ADD COMMENTlink modified 4 months ago by Christophe Dessimoz500 • written 4 months ago by anusblat0
1
gravatar for Christophe Dessimoz
4 months ago by
University College London
Christophe Dessimoz500 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 4 months ago by Christophe Dessimoz500
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1668 users visited in the last hour