Bio::CodonUsage::Table.3pm

Langue: en

Version: 2010-05-19 (ubuntu - 24/10/10)

Section: 3 (Bibliothèques de fonctions)

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:
   http://bugzilla.open-bio.org/
 
 

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