codon preferences

rd at sanger.ac.uk rd at sanger.ac.uk
Sun Oct 2 11:06:24 EST 1994


David Huen asked about C. elegans codon preference tables.

Here are the tables used by Phil Green's program GENEFINDER for
codon preference, as used by the genomic sequencing project.  They
were assembled by LaDeana Hillier and Phil Green at St Louis.  The
original tables used by Genefinder are available in the subdirectory
wgf/ of the ACEDB release.

Table of codon frequences in a number of confirmed coding genes:

    A     C     G     T

A  594   292   478    81  A
   827   581   190   810  C
  1495   169    57   720  G
   618   489   163   658  T
 
C 1098  1008   169    73  A
   332    77   328   721  C
   490   171    71   198  G
   317   143   631   880  T
 
G 1200   371  1465   144  A
   705   822   107   600  C
  1321   134    55   254  G
  1067   988   291   687  T
 
T    0   352     0    86  A
   465   433   310   726  C
     0   266   217   504  G
   296   499   273   277  T

Followed by a table of triplet frequencies as they would occur in
DNA with standard C. elegans diunucleotide frequencies:

    A     C     G     T
A 4635  1446  1601  1730  A
  1439   617   753  1425  C
  1429   719   626  1432  G
  3129  1097  1097  3129  T
 			   
C 1938  1050   995   733  A
   887   375   456   993  C
   922   458   458   922  G
  1432   626   719  1429  T
 			   
G 2307   879  1059   817  A
   736   458   458   736  C
   993   456   375   887  G
  1425   753   617  1439  T
 			   
T 1752  1804  1804  1752  A
   817  1059   879  2307  C
   733   995  1050  1938  G
  1730  1601  1446  4635  T

Genefinder uses the log of the ratio of the values in these two tables
for its per-triplet scores.  Our experience is that C. elegans genes
vary a lot in degree of bias, with many of them showing little or no
bias.  In general it appears that the more biased genes are likely to
be more highly expressed.  There was a Gazette article a couple of
years ago from Chris Fields about this.

Richard Durbin



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