codon usage

[Mike Cherry 726-5955]

In reply to Mark Estelle's question:
>Can anyone suggest a source for Arabidopsis codon usage information. 

I created a codon usage table for Arabidopsis using GenBank 63. The codon 
usage table included below and tables for 46 other organisms can be 
retrieved via anonymous ftp from frodo.mgh.harvard.edu, 
ftp.bio.indiana.edu, and ftp.bchs.uh.edu. The tables are also available on 
the EMBL mail server and others.

I hope to update these tables in the next month or two with sequences from 
GenBank 71.

Mike Cherry
cherry at frodo.mgh.harvard.edu

-----------  ath.cod  -----------------------------------------

Arabidopsis thaliana

31 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.

AmAcid  Codon     Number    /1000     Fraction   ..
 
Gly     GGG       80.00      7.37      0.10
Gly     GGA      292.00     26.89      0.37
Gly     GGT      310.00     28.55      0.39
Gly     GGC      108.00      9.95      0.14
 
Glu     GAG      344.00     31.68      0.56
Glu     GAA      275.00     25.32      0.44
Asp     GAT      278.00     25.60      0.55
Asp     GAC      227.00     20.90      0.45
 
Val     GTG      187.00     17.22      0.25
Val     GTA       60.00      5.53      0.08
Val     GTT      305.00     28.09      0.41
Val     GTC      187.00     17.22      0.25
 
Ala     GCG       84.00      7.74      0.10
Ala     GCA      151.00     13.91      0.19
Ala     GCT      382.00     35.18      0.48
Ala     GCC      184.00     16.94      0.23
 
Arg     AGG      143.00     13.17      0.23
Arg     AGA      209.00     19.25      0.34
Ser     AGT      103.00      9.49      0.13
Ser     AGC      118.00     10.87      0.14
 
Lys     AAG      426.00     39.23      0.67
Lys     AAA      210.00     19.34      0.33
Asn     AAT      127.00     11.70      0.33
Asn     AAC      263.00     24.22      0.67
 
Met     ATG      297.00     27.35      1.00
Ile     ATA       70.00      6.45      0.11
Ile     ATT      257.00     23.67      0.41
Ile     ATC      306.00     28.18      0.48
 
Thr     ACG       82.00      7.55      0.13
Thr     ACA      168.00     15.47      0.26
Thr     ACT      197.00     18.14      0.30
Thr     ACC      199.00     18.33      0.31
 
Trp     TGG      155.00     14.27      1.00
End     TGA       74.00      6.81      0.59
Cys     TGT       93.00      8.56      0.45
Cys     TGC      115.00     10.59      0.55
 
End     TAG       20.00      1.84      0.16
End     TAA       32.00      2.95      0.25
Tyr     TAT       99.00      9.12      0.34
Tyr     TAC      194.00     17.87      0.66
 
Leu     TTG      253.00     23.30      0.26
Leu     TTA       72.00      6.63      0.07
Phe     TTT      145.00     13.35      0.35
Phe     TTC      265.00     24.40      0.65
 
Ser     TCG       92.00      8.47      0.11
Ser     TCA      152.00     14.00      0.19
Ser     TCT      198.00     18.23      0.24
Ser     TCC      157.00     14.46      0.19
 
Arg     CGG       41.00      3.78      0.07
Arg     CGA       52.00      4.79      0.08
Arg     CGT      128.00     11.79      0.21
Arg     CGC       43.00      3.96      0.07
 
Gln     CAG      231.00     21.27      0.53
Gln     CAA      202.00     18.60      0.47
His     CAT       96.00      8.84      0.40
His     CAC      144.00     13.26      0.60
 
Leu     CTG      106.00      9.76      0.11
Leu     CTA       91.00      8.38      0.09
Leu     CTT      257.00     23.67      0.26
Leu     CTC      203.00     18.69      0.21
 
Pro     CCG       85.00      7.83      0.16
Pro     CCA      174.00     16.02      0.33
Pro     CCT      177.00     16.30      0.34
Pro     CCC       84.00      7.74      0.16

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