Translate/convert organism prefix in genes names - eg At_geneA, Dd_geneA etc - to a useful alternative

Question

[Steve Barratt]

I have a huge list of gene names as described in a some supplementary data as:

Hs_GeneA
Mm_GeneA
Dm_GeneA

I have extracted the prefixes (Hs, Mm, Dm etc..) and would like to convert/translate them into a a useful taxonomic identifier, for example convert Mm to the NCBI Taxonomy ID 10090.

Could anyone suggest a tool to accomplish this or a database that might provide this information?

Thanks!

[Zhaorong]

Two letter prefix are sometimes ambiguous (e.g. Tribolium castaneum (red flour beetle) and Theobroma cacao (cacao)). So my guess is that the prefixes you need to deal with are likely to be commonly seen organisms. So you may want to take a look at the NCBI Taxonomy Browser.

Answer 1

[David Westergaard]

Honestly, how many different organisms are there? If there is not too many (<1000), just make a dictionary manually.