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GCG at the HGMP-RC

Martin Hilbers mph at dl.ac.uk
Tue Mar 4 08:02:47 EST 1997


Miss. V Wood wrote:

> GCGFILE:                enzrefs.txt  and enzsources.txt
> GCGDIR:                 gcg/gcgcore/data/moredata/
> CURRENT RELEASE:        v gcgref 608 jul31 96 v commdata 608 jul31 96
> SOURCE SITE:            ?
> SOURCE FILE:            ?
> REFORMATTING:
 
> I have not been able to find new versions of the above files 

enzrefs.txt is distributed with rebase as gcgref.xxx
enzsources.txt is distributed with rebase as commdata.xxx.
(xxx is the release number). You can find these files
at ftp://vent.neb.com/pub/rebase

> GCG is supplied with only 3 codon usage tables:
> mus.cod         rat.cod         template.cod
> 45 additional codon tables are available at the EBI.
> It should be noted that many of these are made with relatively few 
> sequence sand we aim to replace these with the CUTG tables from 
> http://www.dna.go.jp/ which will require conversion to gcg format.

At SEQNET we use a perl script to convert cutg to gcg format. At the 
moment we don't have them directly available for gcg, but rather
have them in a large file, from which entries can be retrieved
using srs. The perl script we use can be found at
http://www.seqnet.dl.ac.uk/srsdoc/getcutg

Cheers,

Martin




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