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A codon quality check tool, it produces a Codon Optimization table to see the quality of each codon.

The simplest way of depiction is to plot the codon usage frequency that can be found in common codon usage tables. A more elaborate way to depict the codon quality is to convert the codon usage frequency into relative adaptiveness values. In contrast to the codon usage frequency the relative adaptiveness takes into account the number of codons which code for the respective amino acid.

Installation from cpan

cpan>install  Bio::Tools::CodonOptTable

depends on GD::Graph and Bio::Perl

USES or Examples

You can use this module in the following ways

use Bio::Tools::CodonOptTable;


                                                -id  => 'GeneFragment-12',
                                                -accession_number => 'Myseq1',
                                                -alphabet => 'dna',
                                                -is_circular => 1,
                                                -genetic_code => 1,

B<#If you wanna read from file>

my $seqobj = Bio::Tools::CodonOptTable->new(-file => "contig.fasta",

                                             -format => 'Fasta',
                                             -genetic_code => 1,

B<#If you have Accession number and want to get file from NCBI>

my $seqobj = Bio::Tools::CodonOptTable->new(-ncbi_id => "J00522",

-genetic_code => 1,);

my $myCodons = $seqobj->rscu_rac_table();


            for my $each_aa (@$myCodons)
        print "Codon      : ",$each_aa->{'codon'},"\t";
        print "Frequency  : ",$each_aa->{'frequency'},"\t";
        print "AminoAcid  : ",$each_aa->{'aa_name'},"\t";
        print "RSCU Value : ",$each_aa->{'rscu'},"\t"; #Relative Synonymous Codons Uses
        print "RAC Value  : ",$each_aa->{'rac'},"\t"; #Relative Adaptiveness of a Codon
        print "\n";

B<# To get the prefered codon list based on RSCU & RAC Values > my $prefered_codons = $seqobj→prefered_codon($myCodons);

while ( my ($amino_acid, $codon) = each(%$prefered_codons) ) {

print "AminoAcid : $amino_acid \t Codon : $codon\n"; }

B<# To produce a graph between RSCU & RAC> # Graph output file extension should be GIF, we support GIF only


bio/tools/codonopttable.1261043159.txt.gz · Last modified: 2010/05/22 14:19 (external edit)