Converting OMA IDs to Ensembl gene names

Question

[Eric]

I fetched a complete list of orthologs between two species using OMAdb in R and it seems there are two main ways the output dataframe distinguishes between genes: omaid and canonicalid.

I want to be able to map the results to my RNAseq dataset which is aligned using Ensembl annotation, so I need a way to convert either the OMA-ID or the Canonical-ID to Ensembl gene names.

The OMA website does that if I search the entry with OMAID and click Gene Information, the right output is labeled under "EnsemblGenomes" but of course I cannot do this one by one since I have an entire genome to cover.

I also noticed multiple OMA-IDs could match to the same Canonical-ID, so even though I had minor success converting Canonical-ID to Ensembl names it doesn't seem ideal.

What is the recommended way to convert OMA-ID to Ensembl gene names?

Answer 1

[Adrian Altenhoff]

Hi, the best option is to use the oma-Enseml crossrefence file from the downloadsection of the Oma Browser: https://omabrowser.org/oma/current/

The direct link of the mapping file is always https://omabrowser.org/All/oma-ensembl.txt.gz

Best wishes

Adrian

[Eric]

Brilliant! Thanks for the swift response!!!