From: CHERRY@FRODO.MGH.HARVARD.EDU (Mike Cherry 726-5955)
Newsgroups: bionet.genome.arabidopsis
Subject: Updated Arabidopsis codon usage table, in GCG format
Date: 16 Aug 92 21:27:16 GMT
Distribution: bionet

I've had several requests for an updated codon usage table of Arabidopsis
since I originally created codon usage tables for many species from 
GenBank 63 two years ago. The table included below represents almost an 8
fold increase in the number of codons available for Arabidopsis and used
to generate the codon usage table. 

The enclosed table, like the original, is in GCG format. I believe it
should be fairly easy to convert this table to formats used by other
software products. 

Mike Cherry

P.S. The ACeDB software used by the AAtDB database will produce a codon
usage table from any set of sequences known to the database. This is an
option of the DNA analysis window.

---------------------------------------------------------

Arabidopsis thaliana codon usage.

Created using 238 coding sequences from GenBank 72 including
updates through June 11, 1992.

Coding regions extracted from AAtDB database version 1.1 using the
ACeDB software version 1.7.

Table constructed using the GCG program CodonFrequency

Questions about this table should be directed to:

J. Michael Cherry
Department of Molecular Biology
Massachusetts General Hospital
cherry@frodo.mgh.harvard.edu

Meaning of the columns:
AmAcid   -  three letter code for the amino acid designated by the codon
Codon    -  Codon sequence
Number   -  Total number of occurances of this codon in the input set
/1000    -  Number of occurances of this codon per 1000 codons in the input set
Fraction -  Fraction of occurance of this codon is used from the set of
            codons representing the same amino acid


AmAcid  Codon     Number    /1000     Fraction   ..
 
Gly     GGG      747.00      9.26      0.12
Gly     GGA     2418.00     29.97      0.38
Gly     GGT     2308.00     28.60      0.36
Gly     GGC      871.00     10.79      0.14
 
Glu     GAG     2675.00     33.15      0.53
Glu     GAA     2337.00     28.96      0.47
Asp     GAT     2516.00     31.18      0.59
Asp     GAC     1719.00     21.30      0.41
 
Val     GTG     1459.00     18.08      0.26
Val     GTA      568.00      7.04      0.10
Val     GTT     2191.00     27.15      0.40
Val     GTC     1319.00     16.35      0.24
 
Ala     GCG      665.00      8.24      0.11
Ala     GCA     1336.00     16.56      0.22
Ala     GCT     2861.00     35.46      0.47
Ala     GCC     1208.00     14.97      0.20
 
Arg     AGG     1027.00     12.73      0.25
Arg     AGA     1305.00     16.17      0.32
Ser     AGT      958.00     11.87      0.15
Ser     AGC      957.00     11.86      0.15
 
Lys     AAG     3161.00     39.17      0.61
Lys     AAA     1989.00     24.65      0.39
Asn     AAT     1319.00     16.35      0.40
Asn     AAC     1968.00     24.39      0.60
 
Met     ATG     2093.00     25.94      1.00
Ile     ATA      724.00      8.97      0.16
Ile     ATT     1857.00     23.01      0.41
Ile     ATC     1935.00     23.98      0.43
 
Thr     ACG      560.00      6.94      0.13
Thr     ACA     1189.00     14.74      0.27
Thr     ACT     1538.00     19.06      0.34
Thr     ACC     1171.00     14.51      0.26
 
Trp     TGG      929.00     11.51      1.00
End     TGA      165.00      2.04      0.44
Cys     TGT      724.00      8.97      0.53
Cys     TGC      634.00      7.86      0.47
 
End     TAG       66.00      0.82      0.18
End     TAA      140.00      1.74      0.38
Tyr     TAT      877.00     10.87      0.38
Tyr     TAC     1423.00     17.64      0.62
 
Leu     TTG     1648.00     20.42      0.23
Leu     TTA      736.00      9.12      0.10
Phe     TTT     1400.00     17.35      0.42
Phe     TTC     1933.00     23.96      0.58
 
Ser     TCG      589.00      7.30      0.10
Ser     TCA     1126.00     13.95      0.18
Ser     TCT     1644.00     20.37      0.27
Ser     TCC      921.00     11.41      0.15
 
Arg     CGG      278.00      3.45      0.07
Arg     CGA      404.00      5.01      0.10
Arg     CGT      822.00     10.19      0.20
Arg     CGC      280.00      3.47      0.07
 
Gln     CAG     1439.00     17.83      0.50
Gln     CAA     1414.00     17.52      0.50
His     CAT      771.00      9.55      0.50
His     CAC      765.00      9.48      0.50
 
Leu     CTG      703.00      8.71      0.10
Leu     CTA      698.00      8.65      0.10
Leu     CTT     1914.00     23.72      0.27
Leu     CTC     1461.00     18.11      0.20
 
Pro     CCG      612.00      7.58      0.16
Pro     CCA     1334.00     16.53      0.35
Pro     CCT     1358.00     16.83      0.35
Pro     CCC      534.00      6.62      0.14