In article <9501252044.AA01273 at asrr>, <rproctor at ASRR.ARSUSDA.GOV> wrote:
>A collegue of mine is looking for a reference for yeast codon preferences.
>Can anyone help? Thanks in advance
>>Can you send responses to me?
>Bob Proctor
>rproctor at asrr.arsusda.gov
Here's a codon usage table I just produced. The "Number" column is
the total number of that codon found in all the exons I processed,
"/1000" is the number of a codon per 1000 codons, and "Fraction" is
the fraction a particular codon is used for its encoded amino acid.
Mike
---------------
Saccharomyces cerevisiae Codon Usage
January 25, 1995
cherry at genome.stanford.edu
This table was built from 1817 exons (822163 codons) contained in the
seven completely sequenced S.c. chromosomes: I, II, III, V, VIII, IX,
and XI. Not all exons from these chromosomes were used. If a problem
was detected the exon was eliminated from this analysis. The GCG
CodonFrequency program was used to produce this table.
AmAcid Codon Number /1000 Fraction ..
Gly GGG 5240.00 6.37 0.13
Gly GGA 9211.00 11.20 0.22
Gly GGT 18381.00 22.36 0.45
Gly GGC 8283.00 10.07 0.20
Glu GAG 16005.00 19.47 0.30
Glu GAA 36533.00 44.44 0.70
Asp GAT 30578.00 37.19 0.65
Asp GAC 16656.00 20.26 0.35
Val GTG 9346.00 11.37 0.20
Val GTA 9930.00 12.08 0.21
Val GTT 17411.00 21.18 0.38
Val GTC 9613.00 11.69 0.21
Ala GCG 5256.00 6.39 0.11
Ala GCA 13423.00 16.33 0.29
Ala GCT 16586.00 20.17 0.36
Ala GCC 10486.00 12.75 0.23
Arg AGG 7808.00 9.50 0.22
Arg AGA 16827.00 20.47 0.47
Ser AGT 11883.00 14.45 0.16
Ser AGC 8461.00 10.29 0.11
Lys AAG 24785.00 30.15 0.42
Lys AAA 34009.00 41.37 0.58
Asn AAT 29130.00 35.43 0.59
Asn AAC 20430.00 24.85 0.41
Met ATG 17171.00 20.89 1.00
Ile ATA 14812.00 18.02 0.28
Ile ATT 24715.00 30.06 0.46
Ile ATC 14156.00 17.22 0.26
Thr ACG 6838.00 8.32 0.14
Thr ACA 14799.00 18.00 0.30
Thr ACT 16817.00 20.45 0.34
Thr ACC 10513.00 12.79 0.21
Trp TGG 8804.00 10.71 1.00
End TGA 422.00 0.51 0.31
Cys TGT 6852.00 8.33 0.62
Cys TGC 4193.00 5.10 0.38
End TAG 298.00 0.36 0.22
End TAA 638.00 0.78 0.47
Tyr TAT 15351.00 18.67 0.56
Tyr TAC 11964.00 14.55 0.44
Leu TTG 22106.00 26.89 0.28
Leu TTA 21161.00 25.74 0.27
Phe TTT 21949.00 26.70 0.59
Phe TTC 15353.00 18.67 0.41
Ser TCG 7380.00 8.98 0.10
Ser TCA 15628.00 19.01 0.21
Ser TCT 19552.00 23.78 0.26
Ser TCC 12003.00 14.60 0.16
Arg CGG 1538.00 1.87 0.04
Arg CGA 2525.00 3.07 0.07
Arg CGT 5166.00 6.28 0.14
Arg CGC 2269.00 2.76 0.06
Gln CAG 10417.00 12.67 0.32
Gln CAA 22054.00 26.82 0.68
His CAT 10992.00 13.37 0.63
His CAC 6538.00 7.95 0.37
Leu CTG 9104.00 11.07 0.12
Leu CTA 10885.00 13.24 0.14
Leu CTT 10249.00 12.47 0.13
Leu CTC 4681.00 5.69 0.06
Pro CCG 4475.00 5.44 0.12
Pro CCA 14551.00 17.70 0.40
Pro CCT 11011.00 13.39 0.31
Pro CCC 5962.00 7.25 0.17
