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Chlamy codon usage table, part 2

Antonio R. Franco bf1rodri at cc.uco.es
Thu Jul 29 06:19:03 EST 1993


	Here goes (as promised) a sample of the output of the "correspond" 
command (from the GCG Wisconsin package) run using the Chlamy codon usage 
tables.
	The entire file is too big to be presented here (over 150.000 
bytes), but it will be at the disposal to whom will be interested by simply 
sending a request to my address.


CORRESPOND
  STATISTIC_USED

     Correspond reads the normalized (/1000)  data from the  fourth column
     of the codon frequency table.  It then totals these  figures for each
     synonymous family.  If the total for a family in either table is 0.0,
     then none of  the codons  from that family contribute anything to the
     value of D squared.

     Frequency(codon)  = Number(column 4) / Total(family)
     
         D squared = Sum over all 64 codons of:
     
         ( Freq(codon,table 1) - Frequency(codon,table 2) ) 2


	To see more details, please check Grantham, NAR 9(1): r43-r74 
(1981).


-------------
 
 CORRESPOND  July 26, 1993  15:27

Between                       and    D-Squared   D   Not-Counted ..

d10542.cod             d10542.cod    0.000000    0.000000   0
d10542.cod             d90206.cod    0.657688    0.810979   0
d10542.cod             j02774.cod    4.785773    2.187641   0
d10542.cod             j05524.cod    1.511386    1.229384   1
d10542.cod             k03281.cod    1.178677    1.085669   0
d10542.cod             l07282.cod    1.511386    1.229384   1
d10542.cod             m10064.cod    1.104133    1.050778   0
d10542.cod             m11447.cod    3.408368    1.846177   0
......
d10542.cod             x52257.cod   15.011325    3.874445   0
d10542.cod             x53574.cod    1.302662    1.141342   0
d10542.cod             x54487.cod    0.657688    0.810979   0
d10542.cod             x54488.cod    0.529464    0.727643   0
d10542.cod             x55382.cod    1.025029    1.012437   0
...............
d90206.cod             x14549.cod    1.578390    1.256340   2
d90206.cod             x15053.cod    2.918266    1.708293   2
d90206.cod             x15164.cod    0.557552    0.746694   4
d90206.cod             x15165.cod    0.755549    0.869223   2
d90206.cod             x15427.cod    1.408689    1.186882   1
d90206.cod             x16180.cod    0.620390    0.787649   0
d90206.cod             x16619.cod    3.082307    1.755650   0
......................
k03281.cod             j05524.cod    0.518019    0.719736   1
k03281.cod             k03281.cod    0.000000    0.000000   0
k03281.cod             l07282.cod    0.518019    0.719736   1
k03281.cod             m10064.cod    0.044958    0.212033   0
k03281.cod             m11447.cod    2.237630    1.495871   0
k03281.cod             m11448.cod    2.203394    1.484383   0
k03281.cod             m15187.cod    0.277109    0.526412   0
k03281.cod             m20729.cod    1.619799    1.272713   3
k03281.cod             m24072.cod    0.413905    0.643354   0
k03281.cod             m25916.cod    2.237630    1.495871   0
k03281.cod             x52257.cod   19.278385    4.390716   0
k03281.cod             x53574.cod    0.202672    0.450192   0
k03281.cod             x54487.cod    0.599445    0.774238   0
.......................
m11448.cod             x15165.cod    2.607206    1.614685   2
m11448.cod             x15427.cod    3.354807    1.831613   1
m11448.cod             x16180.cod    3.402443    1.844571   0
m11448.cod             x16619.cod    4.187582    2.046358   0
m11448.cod             x52257.cod   20.706438    4.550433   0
m11448.cod             x53574.cod    2.325708    1.525027   0
m11448.cod             x54487.cod    2.723251    1.650228   0
m11448.cod             x54488.cod    2.928271    1.711219   0
m11448.cod             x55382.cod    4.162784    2.040290   0
m11448.cod             x57973.cod    5.492990    2.343713   5
........................
m25916.cod             x04471.cod    2.720075    1.649265   2
m25916.cod             x04472.cod    2.583788    1.607417   2
m25916.cod             x12634.cod    5.715916    2.390798   5
m25916.cod             x13495.cod    2.816686    1.678299   0
m25916.cod             x13496.cod    4.470168    2.114277   4
m25916.cod             x13826.cod    2.385484    1.544501   2
m25916.cod             x13832.cod    2.318460    1.522649   4
m25916.cod             x14549.cod    5.223289    2.285451   2
m25916.cod             x15053.cod    1.568086    1.252232   2
m25916.cod             x15164.cod    3.225781    1.796046   4
m25916.cod             x15165.cod    2.763172    1.662279   2
m25916.cod             x15427.cod    3.523758    1.877168   1
m25916.cod             x16180.cod    3.466123    1.861753   0
.................
m25918.cod             m62962.cod    0.270459    0.520057   0
m25918.cod             m67448.cod    6.366172    2.523128   0
m25918.cod             m73493.cod    0.327572    0.572339   3
m25918.cod             m87526.cod    3.678399    1.917915   0
m25918.cod             m94265.cod    1.104133    1.050778   0
m25918.cod             s44199.cod    6.041874    2.458022   0
m25918.cod             x04471.cod    0.308310    0.555256   2
m25918.cod             x04472.cod    0.263409    0.513234   2
m25918.cod             x16619.cod    3.935941    1.983920   0
m25918.cod             x52257.cod   18.741076    4.329096   0
................
x15053.cod             d10542.cod    3.310420    1.819456   2
x15053.cod             d90206.cod    2.918266    1.708293   2
x15053.cod             j02774.cod    2.958225    1.719949   2
x15053.cod             j05524.cod    3.632907    1.906019   3
x15053.cod             k03281.cod    3.258364    1.805094   2
x15053.cod             l07282.cod    3.632907    1.906019   3
x15053.cod             m10064.cod    3.281984    1.811625   2
x15053.cod             m11447.cod    1.568086    1.252232   2
x15053.cod             m11448.cod    1.553389    1.246350   2
x15053.cod             m15187.cod    3.298939    1.816298   2
x15053.cod             m20729.cod    3.841049    1.959859   3
.................
x52257.cod             d10542.cod   15.011325    3.874445   0
x52257.cod             d90206.cod   17.260836    4.154616   0
x52257.cod             j02774.cod   15.185028    3.896797   0
x52257.cod             j05524.cod   17.860167    4.226129   1
x52257.cod             k03281.cod   19.278385    4.390716   0
x52257.cod             l07282.cod   17.860167    4.226129   1
x52257.cod             m10064.cod   18.741076    4.329096   0
x52257.cod             m11447.cod   20.621590    4.541100   0
x52257.cod             m11448.cod   20.706438    4.550433   0
x52257.cod             m15187.cod   18.061649    4.249900   0
...............
x66410.cod             x57973.cod    3.412654    1.847337   5
x66410.cod             x61624.cod    1.348753    1.161358   0
x66410.cod             x62135.cod    4.520462    2.126138   0
x66410.cod             x62335.cod    3.565943    1.888371   5
x66410.cod             x65119.cod    1.615418    1.270991   2
x66410.cod             x66410.cod    0.000000    0.000000   0
x66410.cod             x66412.cod    0.752665    0.867563   0
x66410.cod             x68128.cod    1.037332    1.018495   0
x66412.cod             d10542.cod    1.157538    1.075890   0
x66412.cod             d90206.cod    0.526464    0.725578   0
x66412.cod             j02774.cod    6.270373    2.504071   0




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