In article <4fd65b$sti at flood.weeg.uiowa.edu>, Ken Volk
<kvolk at blue.weeg.uiowa.edu> wrote:
> When using backtranslate, I would like to use a rat specific codon
> frequency table. I have constructed one from 7 rat genes, but I was
> wondering if one has been constructed from many rat genes
There's a whole bucnh available for anonymous ftp at a Mass General
Hospital gopher server (sorry, but I don't have the location handy). Here
is the one for rat codon usage:
Rattus sp. (Rat)
833 genes found in GenBank 63.
Produced by J. Michael Cherry (cherry at frodo.mgh.harvard.edu) with the GCG
program CodonFrequency.
Duplicates, pseudogenes, mutant and synthetic genes were not included.
Coding regions were specified using the Feature Table of each entry, then
checked for accuracy. If more than one stop codon was found the sequence
was not included.
AA Codon Number /1000 Fract
Ala GCG 1441.00 6.08 0.09
Ala GCA 3556.00 14.99 0.21
Ala GCT 5284.00 22.28 0.31
Ala GCC 6579.00 27.74 0.39
Arg AGG 2695.00 11.36 0.22
Arg AGA 2702.00 11.39 0.22
Arg CGG 2121.00 8.94 0.17
Arg CGA 1457.00 6.14 0.12
Arg CGT 1225.00 5.16 0.10
Arg CGC 2301.00 9.70 0.18
Asn AAT 3520.00 14.84 0.39
Asn AAC 5416.00 22.83 0.61
Asp GAT 5021.00 21.17 0.42
Asp GAC 6953.00 29.31 0.58
Cys TGT 2297.00 9.68 0.44
Cys TGC 2941.00 12.40 0.56
Gln CAG 7456.00 31.44 0.75
Gln CAA 2484.00 10.47 0.25
Glu GAG 9776.00 41.22 0.60
Glu GAA 6397.00 26.97 0.40
Gly GGG 3646.00 15.37 0.23
Gly GGA 4015.00 16.93 0.25
Gly GGT 2846.00 12.00 0.18
Gly GGC 5501.00 23.19 0.34
His CAT 2074.00 8.74 0.38
His CAC 3430.00 14.46 0.62
Ile ATA 1367.00 5.76 0.12
Ile ATT 3735.00 15.75 0.33
Ile ATC 6304.00 26.58 0.55
Leu CTG 9240.00 38.96 0.42
Leu CTA 1527.00 6.44 0.07
Leu CTT 2749.00 11.59 0.12
Leu CTC 4583.00 19.32 0.21
Leu TTG 2828.00 11.92 0.13
Leu TTA 1110.00 4.68 0.05
Lys AAG 9423.00 39.73 0.65
Lys AAA 5120.00 21.59 0.35
Met ATG 5928.00 24.99 1.00
Phe TTT 3783.00 15.95 0.39
Phe TTC 5822.00 24.55 0.61
Pro CCG 1380.00 5.82 0.10
Pro CCA 3787.00 15.97 0.29
Pro CCT 3853.00 16.24 0.29
Pro CCC 4166.00 17.56 0.32
Ser AGT 2356.00 9.93 0.13
Ser AGC 4206.00 17.73 0.24
Ser TCG 1063.00 4.48 0.06
Ser TCA 2479.00 10.45 0.14
Ser TCT 3424.00 14.44 0.19
Ser TCC 4146.00 17.48 0.23
Thr ACG 1400.00 5.90 0.10
Thr ACA 3634.00 15.32 0.27
Thr ACT 3216.00 13.56 0.24
Thr ACC 5088.00 21.45 0.38
Trp TGG 3319.00 13.99 1.00
Tyr TAT 2753.00 11.61 0.40
Tyr TAC 4146.00 17.48 0.60
Val GTG 7246.00 30.55 0.48
Val GTA 1554.00 6.55 0.10
Val GTT 2391.00 10.08 0.16
Val GTC 3872.00 16.32 0.26
End TGA 610.00 2.57 0.58
End TAG 188.00 0.79 0.18
End TAA 257.00 1.08 0.24
Cheers,
AJW
----------------
John Watson
Bristol-Myers Squibb Co.
watson_j at bms.com
---------------------------------------------------------------------
"If you're not part of the solution, you're part of the precipitate."
---------------------------------------------------------------------
