IUBio Biosequences .. Software .. Molbio soft .. Network News .. FTP

Chlamydomonas codon usage table

Antonio R. Franco bf1rodri at cc.uco.es
Tue Jul 27 13:57:17 EST 1993

	Here goes a Chlamydomonas codon usage table in the GCG format


	i) The sequences herein used have been extracted from the feature 
           tables of sequences taken from the GenBank database release 76.
	   Only sequences from Chlamydomonas reinhardtii have been 

	ii) Notice the number of stop codons are equal to the number of 
	    total sequences but one, since sequence X62335 is an uncomplete 
	    sequence. This way I am sure there is not failure and/or false 

	iii) The individual codon usage tables have been additionally checked 
	     with the command "correspond" from the GCG. This statitical 
	     program compares the usage tables, giving values which get smaller
	     as the patterns of codon usage become more similar (see Grantham,
	     NAR 9(1) r43-r74 (1981)). If an aminoacid is not used at all in 
	     one of the tables, its codons contribute nothing to the sum of
	     squares. These ignored codons are ignored and reported. This 
	     study can be considered as another way of testing the absence 
	     of failures in introducing the ORF's of the sequences considered. 

		To output of the command "correspond" run with all of the 
	     codon usage tables is posted in a separate message. In order 
	     to show how the "correspond" analysis works, I have 
	     intentionally introduced in the analysis a chloroplastic sequence,
	     X52257. Notice the much higher values of the statitical 
	     parameter found when we compare this chloroplastic sequence 
	     with the rest of the sequences. I must insist, however, the codon
	     usage table shown below DO NOT CONTAIN THE INFORMATION OF SEQUENCE
	     X52257. Only nuclear genes (including signal peptides) have 
	     been taken in account.

 CODONFREQUENCY  July 26, 1993  16:09

 From an existing codon frequency file: d10542.cod  FileCheck: 8270

 CODONFREQUENCY  July 22, 1993  12:37

More information about the Chlamy mailing list

Send comments to us at biosci-help [At] net.bio.net