and geneticcode database ?

Peter Rice pmr at sanger.ac.uk
Thu Nov 12 11:51:32 EST 1998


gbottu at bigben.vub.ac.be (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 http://www.ncbi.nlm.nih.gov:6224/DIRSUB/gc.prt seems not to be
> available anymore and is maybe not in the right format.

The file is at:

ftp://ncbi.nlm.nih.gov/entrez/misc/data/gc.prt

geneticcode.is 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"
"SGC5"
6

"Protozoan Mitochondrial (and Kinetoplast)"
"SGC6"
7

"[OBSOLETE, posttranscriptional editing only] Plant Mitochondrial/Chloroplast"
"SGC7"
8

"Euplotid Macronuclear"
"SGC9"
10

"Eubacterial"
11

"Group II yeasts (Nuc Acids Res 1993, 21:4039)"
12


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




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