I have a list of species names in NCBI format...:
NC010572:2102295-2103827:StreptomycesgriseusNBRC13350 NC003155:3077206-3078735:Streptomycesavermitilis NC002678:2750005-2751465:Mesorhizobiumloti NC009636:2588398-2589875:SinorhizobiummedicaeWSM419 NC003047:81767-83250:Sinorhizobiummeliloti NC010994:3677840-3679352:RhizobiumetliCIAT652 NC007761:3576324-3577836:RhizobiumetliCFN_42
that I would like to convert to KEGG's three letter species name format:
nmr csy neq kcr hah
(Note that the examples are not actually an example of this mapping, just an example of each separate format).
Thanks
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User 2385 •
2 answers
There are a few ways to do this at the KEGG website:
- List of complete genomes with species and 3 letter codes
- Search organisms with option to download HTML for parsing
- Browse/search the organism taxonomy
I guess the HTML download is the best option for a computational approach (parse your list of species and match to the file). There may be other useful files for download from KEGG, but I'm uncertain as to their availability now that parts of KEGG are no longer free.
If one would still land on this elderly post: There's now handy tool on uniprot website, that allows between database translations of ID. I think it covers all of them.
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