Codon usage tables available
J. Michael Cherry
Cherry at Frodo.MGH.Harvard.EDU
Mon Feb 18 20:14:38 EST 1991
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 220.127.116.11). 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.
cherry at frodo.mgh.harvard.edu
Department of Molecular Biology
Massachusetts General Hospital, Boston
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