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BioPerl-1.6.920
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/ Bio::CodonUsage::Table

NAME

Bio::CodonUsage::Table - for access to the Codon usage Database at http://www.kazusa.or.jp/codon.

SYNOPSIS

use Bio::CodonUsage::Table;
use Bio::DB::CUTG;
use Bio::CodonUsage::IO;
use Bio::Tools::SeqStats;

# Get  a codon usage table from web database
my $cdtable = Bio::DB::CUTG->new(-sp => 'Mus musculus',
                                 -gc => 1);

# Or from local file
my $io      = Bio::CodonUsage::IO->new(-file => "file");
my $cdtable = $io->next_data();

# Or create your own from a Bio::PrimarySeq compliant object,
# $codonstats is a ref to a hash of codon name /count key-value pairs
my $codonstats = Bio::Tools::SeqStats->count_codons($Seq_objct);

# '-data' must be specified, '-species' and 'genetic_code' are optional
my $CUT = Bio::CodonUsage::Table->new(-data    => $codonstats,
                                      -species => 'Hsapiens_kinase');

print "leu frequency is ", $cdtable->aa_frequency('LEU'), "\n";
print "freq of ATG is ", $cdtable->codon_rel_frequency('ttc'), "\n";
print "abs freq of ATG is ", $cdtable->codon_abs_frequency('ATG'), "\n";
print "number of ATG codons is ", $cdtable->codon_count('ATG'), "\n";
print "GC content at position 1 is ", $cdtable->get_coding_gc('1'), "\n";
print "total CDSs for Mus musculus  is ", $cdtable->cds_count(), "\n";

DESCRIPTION

This class provides methods for accessing codon usage table data.

All of the methods at present are simple look-ups of the table or are derived from simple calculations from the table. Future methods could include measuring the codon usage of a sequence , for example, or provide methods for examining codon usage in alignments.

SEE ALSO

Bio::Tools::CodonTable, Bio::WebAgent, Bio::CodonUsage::IO, Bio::DB::CUTG

FEEDBACK

Mailing Lists

User feedback is an integral part of the evolution of this and other Bioperl modules. Send your comments and suggestions preferably to one of the Bioperl mailing lists. Your participation is much appreciated.

bioperl-l@bioperl.org                  - General discussion
http://bioperl.org/wiki/Mailing_lists  - About the mailing lists

Support

Please direct usage questions or support issues to the mailing list:

bioperl-l@bioperl.org

rather than to the module maintainer directly. Many experienced and reponsive experts will be able look at the problem and quickly address it. Please include a thorough description of the problem with code and data examples if at all possible.

Reporting Bugs

Report bugs to the Bioperl bug tracking system to help us keep track the bugs and their resolution. Bug reports can be submitted via the web:

https://redmine.open-bio.org/projects/bioperl/

AUTHORS

Richard Adams, Richard.Adams@ed.ac.uk

APPENDIX

The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _

new

Title   : new
Usage   : my $cut = Bio::CodonUsage::Table->new(-data => $cut_hash_ref,
                                                -species => 'H.sapiens_kinase'
                                                -genetic_code =>1);
Returns : a reference to a new  Bio::CodonUsage::Table object
Args    : none or a reference to a hash of codon counts. This constructor is
          designed to be compatible with the output of
          Bio::Tools::SeqUtils::count_codons()
          Species and genetic code parameters can be entered here or via the 
          species() and genetic_code() methods separately.

all_aa_frequencies

Title   : all_aa_frequencies
Usage   : my $freq = $cdtable->all_aa_frequencies();
Returns : a reference to a hash where each key is an amino acid
          and each value is its frequency in all proteins in that
          species.
Args    : none

codon_abs_frequency

Title   : codon_abs_frequency
Usage   : my $freq = $cdtable->codon_abs_frequency('CTG');
Purpose : To return the frequency of that codon as a percentage
          of all codons in the organism. 
Returns : a percentage frequency
Args    : a non-ambiguous codon string

codon_rel_frequency

Title   : codon_rel_frequency
Usage   : my $freq = $cdtable->codon_rel_frequency('CTG');
Purpose : To return the frequency of that codon as a percentage
          of codons coding for the same amino acid. E.g., ATG and TGG
          would return 100 as those codons are unique.
Returns : a percentage frequency
Args    : a non-ambiguous codon string

probable_codons

Title    : probable_codons
Usage    : my $prob_codons = $cd_table->probable_codons(10);
Purpose  : to obtain a list of codons for the amino acid above a given
           threshold % relative frequency
Returns  : A reference to a hash where keys are 1 letter amino acid  codes
           and values are references to arrays of codons whose frequency
           is above the threshold.
Arguments: a minimum threshold frequency

most_common_codons

Title    : most_common_codons
Usage    : my $common_codons = $cd_table->most_common_codons();
Purpose  : To obtain the most common codon for a given amino acid
Returns  : A reference to a hash where keys are 1 letter amino acid codes
           and the values are the single most common codons for those amino acids
Arguments: None

codon_count

Title   : codon_count
Usage   : my $count = $cdtable->codon_count('CTG');
Purpose : To obtain the absolute number of the codons in the
          organism. 
Returns : an integer
Args    : a non-ambiguous codon string

get_coding_gc

Title   : get_coding_gc
Usage   : my $count = $cdtable->get_coding_gc(1);
Purpose : To return the percentage GC composition for the organism at
          codon positions 1,2 or 3, or an average for all coding sequence
         ('all').
Returns : a number (%-age GC content) or 0 if these fields are undefined
Args    : 1,2,3 or 'all'.

set_coding_gc

Title   : set_coding_gc
Usage   : my $count = $cdtable->set_coding_gc(-1=>55.78);
Purpose : To set the percentage GC composition for the organism at
          codon positions 1,2 or 3, or an average for all coding sequence
          ('all').  
Returns : void
Args    : a hash where the key must be 1,2,3 or 'all' and the value the %age GC
          at that codon position..

species

Title     : species
Usage     : my $sp = $cut->species();
Purpose   : Get/setter for species name of codon table
Returns   : Void or species name string
Args      : None or species name string

genetic_code

Title     : genetic_code
Usage     : my $sp = $cut->genetic_code();
Purpose   : Get/setter for genetic_code name of codon table
Returns   : Void or genetic_code id, 1 by default
Args      : None or genetic_code id, 1 by default if invalid argument.

cds_count

Title   : cds_count
Usage   : my $count = $cdtable->cds_count();
Purpose : To retrieve the total number of CDSs used to generate the Codon Table
          for that organism. 
Returns : an integer
Args    : none (if retrieving the value) or an integer( if setting ).

aa_frequency

Title   : aa_frequency
Usage   : my $freq = $cdtable->aa_frequency('Leu');
Purpose : To retrieve the frequency of an amino acid in the organism
Returns : a percentage
Args    : a 1 letter or 3 letter string representing the amino acid

common_codon

Title   : common_codon
Usage   : my $freq = $cdtable->common_codon('Leu');
Purpose : To retrieve the frequency of the most common codon of that aa
Returns : a percentage
Args    : a 1 letter or 3 letter string representing the amino acid

rare_codon

Title   : rare_codon
Usage   : my $freq = $cdtable->rare_codon('Leu');
Purpose : To retrieve the frequency of the least common codon of that aa
Returns : a percentage
Args    : a 1 letter or 3 letter string representing the amino acid