gilbertd@cricket.bio.indiana.edu (Don Gilbert) (02/18/91)
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 obtain them via anonymous ftp to iubio.bio.indiana.edu, cd [archive.molbio.codon] mget * (to get all 50 files plus the read.me which identifies species) -- Don -- Don Gilbert gilbert@bio.indiana.edu biocomputing office, biology dept., indiana univ., bloomington, in 47405
Cherry@Frodo.MGH.Harvard.EDU (J. Michael Cherry) (02/19/91)
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)