Question: Translate/convert organism prefix in genes names - eg At_geneA, Dd_geneA etc - to a useful alternative
1
gravatar for Steve Barratt
4.3 years ago by
Glasgow, UK
Steve Barratt30 wrote:

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!

database gene • 1.4k views
ADD COMMENTlink modified 4.3 years ago by David Westergaard1.4k • written 4.3 years ago by Steve Barratt30

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

ADD REPLYlink written 4.3 years ago by Zhaorong1.2k
0
gravatar for David Westergaard
4.3 years ago by
Copenhagen, Denmark
David Westergaard1.4k wrote:

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

ADD COMMENTlink written 4.3 years ago by David Westergaard1.4k
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