Codon usage table for Fish

Rodrigo Lopez rodrigol at
Mon Dec 30 11:16:09 EST 1991

In article <1991Dec29.083543.177 at>, inna at writes:
>  Does anyone have codon usage table for Fish, or know FTP site I can get
> it from? It isn't found among codon usage tables on
>  Thanks.
> ----------------------------------------------------------------------
>  Inna Perlov 			   Phone      972-2-584848
>  Hebrew University 		   E-Mail    Inna at hujivms.bitnet
>  Computation center			     Inna at
>  Givat-Ram 91904 Jerusalem	   FAX	      972-2-527349
>  Israel
> ----------------------------------------------------------------------

I found this message using WAIS and hope it you may get the codon usage table
for fish you need.

Here follows the message:

------------------------------------cut here
From: Cherry at Frodo.MGH.Harvard.EDU (J. Michael Cherry)
Newsgroups: bionet.general
Subject: Re: Codon usage tables available
Message-ID: <5755 at>
Date: 19 Feb 91 01:14:38 GMT
References: <1991Feb17.203115.7949 at>
Sender: news at
Organization: Molecular Biology, Mass. General Hospital
Lines: 29

In article <1991Feb17.203115.7949 at> 
gilbertd at (Don Gilbert) writes:
> Mike Cherry (cherry at 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: (IP number Look in the [.codon] 
directory, the 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
exons I manually eliminate all redundant entries and any sequence that
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 at
Department of Molecular Biology
Massachusetts General Hospital, Boston
(a Macintosh news reader user, this message comes from HyperCard


* RODRIGO LOPEZ SERRANO              Biotechnology Centre of Oslo       
* Tel: xx-02-958766                  Gaustadalleen 21                   
* Fax: xx-02-694130                  P.B. 1125 Blindern                 
*                                    0316 Oslo 3 Norway                 
* rodrigol at                                                
* rodrigol at                                                 

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