NAME

Bio::Tools::CodonOptTable - A more elaborative way to check the codons quality

VERSION

Version 0.01

SYNOPSIS

We produces each codon frequency, Relative Synonymous Codons Uses and Relative Adaptiveness of a Codon table and bar graph

that will help you to calculate the Codon Adaptation Index (CAI) of a gene, to see the gene expression level.

Perhaps a little code snippet.

            

              
              
   use Bio::Tools::CodonOptTable;
   my $seqobj = Bio::Tools::CodonOptTable->new ( -seq => 'ATGGGGTGGGCACCATGCTGCTGTCGTGAATTTGGGCACGATGGTGTACGTGCTCGTAGCTAGGGTGGGTGGTTTG',
                           -id  => 'GeneFragment-12',
                           -accession_number => 'Myseq1',
                           -alphabet => 'dna',
                           -is_circular => 1
                           );
   #If you wanna read from file
     
   my $seqobj = Bio::Tools::CodonOptTable->new(-file => "contig.fasta",
                                            -format => 'Fasta');
     
   #If you have Accession number and want to get file from NCBI
     
   my $seqobj = Bio::Tools::CodonOptTable->new(-ncbi_id => "J00522");
     
   my $myCodons = $seqobj->rscu_rac_table();
     
   if($myCodons)
{
    for my $a (@$myCodons)
            {
                print "Codon      : ",$each_aa->[1]->{'codon'},"\t";
                print "Frequency  : ",$each_aa->[1]->{'frequency'},"\t";
                print "AminoAcid  : ",$each_aa->[1]->{'aa_name'},"\t";
                print "RSCU Value : ",$each_aa->[1]->{'rscu'},"\t"; #Relative Synonymous Codons Uses
                print "RAC Value  : ",$each_aa->[1]->{'rac'},"\t"; #Relative Adaptiveness of a Codon
                print "\n";
            }
}
     
   # to produce a graph between RSCU & RAC
   # Graph output file extension should be GIF, we support GIF only
     
   $seqobj->generate_graph($myCodons,"myoutput.gif");
     
   ...
            
          

METHODS

            

              
              
Title   : new
     
Usage1   : $seq    = Bio::Tools::CodonOptTable->new( -seq => 'ATGGGGGTGGTGGTACCCT',
              -id  => 'human_id',
              -accession_number => 'AL000012',
              );
                                               
Usage2   : $seq    = Bio::Tools::CodonOptTable->new( -file => 'myseq.fasta',
              -format => 'fasta',
              );
                                               
Usage3   : $seq    = Bio::Tools::CodonOptTable->new( -ncbi_id => 'J00522');
                                               
Function: Returns a new primary seq object from
   basic constructors, being a string for the sequence
   and strings for id and accession_number.
             
Returns : a new Bio::PrimarySeq object
     
Args    : -seq          => sequence string
   -display_id          => display id of the sequence (locus name) 
   -accession_number => accession number
   -primary_id          => primary id (Genbank id)
   -desc                => description text
   -alphabet            => molecule type (dna,rna,protein)
   -id                  => alias for display id
   -file                => file location
   -format              => file format
   -ncbi_id             => NCBI accession number
               
Note    : IF you are reading sequence from file it will call _read_localfile method
   IF you are fetching file form NCBI it will call _read_remotefile method
            
          

METHODS

            

              
              
Title   : calculate_rscu
                                               
Function: Calculate the RSCU(Relative Synonymous Codons Uses).
                       
Note    : The formula is used in the following references.
 http://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pubmed&pubmedid=3547335
            
          

METHODS

            

              
              
Title   : calculate_rac
                                               
Function: Calculate the RAC(Relative Adaptiveness of a Codon).
                       
Note    : The formula is used in the following references.
 http://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pubmed&pubmedid=3547335
            
          

METHODS

            

              
              
Title   : generate_graph
                                               
Function: Produce a bar graph between RAC(Relative Adaptiveness of a Codon) & RSCU(Relative Synonymous Codons Uses).
            
          

AUTHOR

Rakesh Kumar Shardiwal, <rakesh.shardiwal at gmail.com>

BUGS

Please report any bugs or feature requests to bug-bio-tools-codonopttable at rt.cpan.org, or through the web interface at http://rt.cpan.org/NoAuth/ReportBug.html?Queue=Bio-Tools-CodonOptTable. I will be notified, and then you'll automatically be notified of progress on your bug as I make changes.

SUPPORT

You can find documentation for this module with the perldoc command.

            

              
              
perldoc Bio::Tools::CodonOptTable
            
          

You can also look for information at:

• RT: CPAN's request tracker

  http://rt.cpan.org/NoAuth/Bugs.html?Dist=Bio-Tools-CodonOptTable

• AnnoCPAN: Annotated CPAN documentation

  http://annocpan.org/dist/Bio-Tools-CodonOptTable

• CPAN Ratings

  http://cpanratings.perl.org/d/Bio-Tools-CodonOptTable

• Search CPAN

  http://search.cpan.org/dist/Bio-Tools-CodonOptTable/

ACKNOWLEDGEMENTS

Lalchand Kumawat <lalchand82@gmail.com> Rajneesh Kumar Sharma <biorajneesh@gmail.com>

COPYRIGHT & LICENSE

Copyright 2008 Rakesh Kumar Shardiwal, all rights reserved.

This program is free software; you can redistribute it and/or modify it under the same terms as Perl itself.

cpanm Bio::Tools::CodonOptTable

perl -MCPAN -e shell
install Bio::Tools::CodonOptTable