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From: Cherry@Frodo.MGH.Harvard.EDU (J. Michael Cherry)
Newsgroups: comp.archives
Subject: [bionet] Re: Codon usage tables available
Message-ID: <1991Feb19.050647.20051@ox.com>
Date: 19 Feb 91 05:06:47 GMT
References: <1991Feb17.203115.7949@bronze.ucs.indiana.edu> <5755@husc6.harvard.edu>
Sender: emv@ox.com (Edward Vielmetti)
Reply-To: Cherry@Frodo.MGH.Harvard.EDU (J. Michael Cherry)
Followup-To: bionet.general
Organization: Molecular Biology, Mass. General Hospital
Lines: 35
Approved: emv@ox.com (Edward Vielmetti)
X-Original-Newsgroups: bionet.general

Archive-name: bionet/molbio/genbank-codon-tables/1991-02-19
Archive-directory: frodo.mgh.harvard.edu:[.codon] [132.183.190.10]
Original-posting-by: Cherry@Frodo.MGH.Harvard.EDU (J. Michael Cherry)
Original-subject: Re: Codon usage tables available
Reposted-by: emv@ox.com (Edward Vielmetti)

In article <1991Feb17.203115.7949@bronze.ucs.indiana.edu> 
gilbertd@cricket.bio.indiana.edu (Don Gilbert) writes:
> Mike Cherry (cherry@frodo.mgh.harvard.edu) has produced a set of
> codon usage tables for 50 different species from Genbank release
> 63, which he as generously made publicly available.  These tables
> are useable directly with the GCG software programs which ask for
> codon tables.   

You can retrieve these codon usage tables for all the major species 
reported in GenBank directly from my machine via anonymous ftp: 
frodo.mgh.harvard.edu (IP number 132.183.190.10). Look in the [.codon] 
directory, the read.me file lists which files go with which species.

I'll be updating these codon usage tables in a month or two, probably 
after GenBank release 67.

I use the features table to get the coding regions then check that each 
coding region doesn't have more than one stop codon. From these extracted 
exons I manually eliminate all redundant entries and any sequence that is 
not wild type. This means I remove mutant genes, pseudogenes, viral and 
transposon sequences and those that are questionable. Then I remove all 
but one copy per type of things like immunoglobulins.

Mike Cherry
cherry@frodo.mgh.harvard.edu
Department of Molecular Biology
Massachusetts General Hospital, Boston
617-726-5955
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