Skip site navigation (1)Skip section navigation (2)

FreeBSD Manual Pages

  
 
  

home | help
Bio::CodonUsage::TableUser Contributed Perl DocumentaBio::CodonUsage::Table(3)

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://github.com/bioperl/bioperl-live/issues

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 v5.24.1			  2017-07-08	     Bio::CodonUsage::Table(3)

NAME | SYNOPSIS | DESCRIPTION | SEE ALSO | FEEDBACK | AUTHORS | APPENDIX

Want to link to this manual page? Use this URL:
<https://www.freebsd.org/cgi/man.cgi?query=Bio::CodonUsage::Table&sektion=3&manpath=FreeBSD+12.0-RELEASE+and+Ports>

home | help