and geneticcode database ?

Peter Rice pmr at
Thu Nov 12 11:51:32 EST 1998

gbottu at (Guy Bottu) writes:

> I have just retrieved the taxonomy database from the EBI anonymous ftp server
> (thanks, Nicole Redaschi !), but I have a new problem : taxonomy contains
> links to geneticcode. Where can we find a suitable version of geneticcode ?
> The file seems not to be
> available anymore and is maybe not in the right format.

The file is at: needs minor editing because the file uses tabs:

Change all 3 cases of ' {' to '\t{'

P.S. Thanks to NCBI for the acknowledgement :-)

Now, when I build the links from taxonomy to geneticcode,
how come I get only 6/12 genetic codes linked?

The missing ones are listed below. They include "Eubacterial" - i.e. all
the bacteria (which have alternate start codons GTG, CTG and TTG).

getz 'geneticcode ! (geneticcode < taxonomy)' -f name -f id
"Ciliate Macronuclear and Daycladacean"

"Protozoan Mitochondrial (and Kinetoplast)"

"[OBSOLETE, posttranscriptional editing only] Plant Mitochondrial/Chloroplast"

"Euplotid Macronuclear"


"Group II yeasts (Nuc Acids Res 1993, 21:4039)"

Peter Rice                | Informatics Division, The Sanger Centre,
E-mail: pmr at  | Wellcome Trust Genome Campus,
Tel: (44) 1223 494967     | Hinxton, Cambridge, CB10 1SA, England
Fax: (44) 1223 494919     | URL:

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