Codon usage table for Fish

Rodrigo Lopez rodrigol at ulrik.uio.no
Mon Dec 30 11:16:09 EST 1991


In article <1991Dec29.083543.177 at vms.huji.ac.il>, inna at vms.huji.ac.il 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 nic.funet.fi.
>  Thanks.
> 
> ----------------------------------------------------------------------
>  Inna Perlov 			   Phone      972-2-584848
>  Hebrew University 		   E-Mail    Inna at hujivms.bitnet
>  Computation center			     Inna at vms.huji.ac.il
>  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
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Path:
bionet!uwm.edu!cs.utexas.edu!yale!hsdndev!husc6!Frodo.MGH.Harvard.EDU!Ch
herry
From: Cherry at Frodo.MGH.Harvard.EDU (J. Michael Cherry)
Newsgroups: bionet.general
Subject: Re: Codon usage tables available
Message-ID: <5755 at husc6.harvard.edu>
Date: 19 Feb 91 01:14:38 GMT
References: <1991Feb17.203115.7949 at bronze.ucs.indiana.edu>
Sender: news at husc6.harvard.edu
Organization: Molecular Biology, Mass. General Hospital
Lines: 29

In article <1991Feb17.203115.7949 at bronze.ucs.indiana.edu> 
gilbertd at cricket.bio.indiana.edu (Don Gilbert) writes:
> Mike Cherry (cherry at 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 at frodo.mgh.harvard.edu
Department of Molecular Biology
Massachusetts General Hospital, Boston
617-726-5955
(a Macintosh news reader user, this message comes from HyperCard
NetNews)

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* RODRIGO LOPEZ SERRANO              Biotechnology Centre of Oslo       
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* Tel: xx-02-958766                  Gaustadalleen 21                   
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* Fax: xx-02-694130                  P.B. 1125 Blindern                 
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*                                    0316 Oslo 3 Norway                 
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* rodrigol at biomed.uio.no                                                
*
* rodrigol at ulrik.uio.no                                                 
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