Question: OMA - How to retrieve orthologs of only one representative of each taxonomy rank?
0
gravatar for anusblat
23 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 • 520 views
ADD COMMENTlink modified 23 months ago by Christophe Dessimoz660 • written 23 months ago by anusblat0
1
gravatar for Christophe Dessimoz
23 months ago by
University College London
Christophe Dessimoz660 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 23 months ago by Christophe Dessimoz660

Thanks Christophe,

I just read this reply a bit late. Sorry. Do you know if your answer can be done via website?

Alejandro

ADD REPLYlink written 8 weeks ago by anusblat0

Not currently. But we have in the meantime released packages for Python and R, which should make it even more easy to perform the kind of specific search you seem to be looking to do:

https://f1000research.com/articles/8-42

ADD REPLYlink written 8 weeks ago by Christophe Dessimoz660
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