Here goes a Chlamydomonas codon usage table in the GCG format
CONSIDERATIONS:
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
considered.
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
ORF's.
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
