Cherry@Frodo.MGH.Harvard.EDU (J. Michael Cherry) (02/19/91)
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 (a Macintosh news reader user, this message comes from HyperCard NetNews)