OMA - How to retrieve orthologs of only one representative of each taxonomy rank?

Question

[anusblat]

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

Answer 1

[Christophe Dessimoz]

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.

[anusblat]

Thanks Christophe,

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

Alejandro

[Christophe Dessimoz]

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