Bio::CodonUsage::Table(3pm)				User Contributed Perl Documentation			       Bio::CodonUsage::Table(3pm)

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

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

perl v5.14.2							    2012-03-02					       Bio::CodonUsage::Table(3pm)