I have a long list of NCBI taxonomic ids for organisms and I want to write a script to get their corresponding translation tables. Is there a way to do this through Entrez?

(packages in R, Python etc. would be fine too)


You can find them here at least: https://www.ncbi.nlm.nih.gov/Taxonomy/Utils/wprintgc.cgi

You can download the complete list of codes (using FTP) here.

However, to link a specific organism to a specific codon usage table, you'll need to do a bit of extra work. Perhaps the script here can give you a starting point?

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    $\begingroup$ What I was really looking for was some way to input the taxonomic id/name of an organism and have its translation table returned. NCBI does seem to have this data for specific taxa, because a button on the page you linked ('Genetic Code in Taxonomy Tree') matches organisms with translation tables. $\endgroup$ Nov 8 '21 at 7:16
  • $\begingroup$ Yeah, you'd need to code that together using an ASN.1 parser I guess? $\endgroup$
    – Dan Bolser
    Nov 8 '21 at 12:07

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