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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