IUBio

codon frequency tables

Peter Rice pmr at sanger.ac.uk
Fri Jun 18 04:07:53 EST 1999


proy at rsvs.ulaval.ca (Paul Roy) writes:

> Dear GCGers:
>      Do you know of anyone who has a database of codon frequency tables in
> GCG format?  There was a large database of tables at a Japanese site (but
> not in GCG format) and a smaller one (which our system lost when version
> 10 was installed) which originally came from EGCG version 8.1.  I don't
> know if it would still be available at EBI.  Or has anyone written a
> program to reformat the Japanese database?

The EGCG one included some files that were already generated by
scientists at EMBL but mainly (the files with the 3 letter names) from
the TRANSTERM database (maybe not an obvious place to look) now
available from ftp://ftp.ebi.ac.uk/pub/databases/transterm/

There is now a database generated from Genbank called CUTG which is
indexed on various SRS servers. File cutg.dat is in GCG format but all
in one file. SRS can extract the files for you, or you can use a
simple script to write individual files. There was one available from
http://www.seqnet.dl.ac.uk/srsdoc/getcutg but sadly SEQnet has moved
so the URL does not work any longer. There are over 7000 codon usage
tables in this database.

CUTG's home page is:

http://www.dna.affrc.go.jp/~nakamura/codon.html 

ftp://ftp.dna.affrc.go.jp/pub/codon/current/

-- 
----------------------------------------------------------------------
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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