debian man page for bio::tools::iupac

Bio::Tools::IUPAC(3pm)					User Contributed Perl Documentation				    Bio::Tools::IUPAC(3pm)

NAME
       Bio::Tools::IUPAC - Generates unique Seq objects from an ambiguous Seq object

SYNOPSIS
	use Bio::Seq;
	use Bio::Tools::IUPAC;

	my $ambiseq = Bio::Seq->new(-seq => 'ARTCGUTGR', -alphabet => 'dna');
	my $stream  = Bio::Tools::IUPAC->new(-seq => $ambiseq);

	while ($uniqueseq = $stream->next_seq()) {
	    # process the unique Seq object.
	}

DESCRIPTION
       IUPAC is a tool that produces a stream of unique, "strict"-satisfying Seq objects from an ambiquous Seq object (containing non-standard
       characters given the meaning shown below)

	       Extended DNA / RNA alphabet :
	       (includes symbols for nucleotide ambiguity)
	       ------------------------------------------
	       Symbol	    Meaning	 Nucleic Acid
	       ------------------------------------------
		A	     A		 Adenine
		C	     C		 Cytosine
		G	     G		 Guanine
		T	     T		 Thymine
		U	     U		 Uracil
		M	   A or C
		R	   A or G
		W	   A or T
		S	   C or G
		Y	   C or T
		K	   G or T
		V	 A or C or G
		H	 A or C or T
		D	 A or G or T
		B	 C or G or T
		X      G or A or T or C
		N      G or A or T or C

	       IUPAC-IUB SYMBOLS FOR NUCLEOTIDE NOMENCLATURE:
		 Cornish-Bowden(1985) Nucl. Acids Res. 13: 3021-3030.

       -----------------------------------

	      Amino Acid alphabet:
	       ------------------------------------------
	       Symbol		Meaning
	       ------------------------------------------
	       A	Alanine
	       B	Aspartic Acid, Asparagine
	       C	Cystine
	       D	Aspartic Acid
	       E	Glutamic Acid
	       F	Phenylalanine
	       G	Glycine
	       H	Histidine
	       I	Isoleucine
	       J	Isoleucine/Leucine
	       K	Lysine
	       L	Leucine
	       M	Methionine
	       N	Asparagine
	       O	Pyrrolysine
	       P	Proline
	       Q	Glutamine
	       R	Arginine
	       S	Serine
	       T	Threonine
	       U	Selenocysteine
	       V	Valine
	       W	Tryptophan
	       X	Unknown
	       Y	Tyrosine
	       Z	Glutamic Acid, Glutamine
	       *	Terminator

	       IUPAC-IUP AMINO ACID SYMBOLS:
		 Biochem J. 1984 Apr 15; 219(2): 345-373
		 Eur J Biochem. 1993 Apr 1; 213(1): 2

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/

AUTHOR - Aaron Mackey
       Email amackey-at-virginia.edu

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

   new
	Title	: new
	Usage	: Bio::Tools::IUPAC->new( $seq)
	Function: returns a new seq stream (akin to SeqIO)
	Returns : a Bio::Tools::IUPAC stream object that will produce unique
		  Seq objects on demand.
	Args	: an ambiguously coded Seq.pm object that has a specified 'alphabet'

   next_seq
	Title	: next_seq
	Usage	: $iupac->next_seq()
	Function: returns the next unique Seq object
	Returns : a Seq.pm object
	Args	: none.

   iupac_iup
	Title	: iupac_iup
	Usage	: my %aasymbols = $iupac->iupac_iup
	Function: Returns a hash of PROTEIN symbols -> symbol components
	Returns : Hash
	Args	: none

   iupac_iub
	Title	: iupac_iub
	Usage	: my %dnasymbols = $iupac->iupac_iub
	Function: Returns a hash of DNA symbols -> symbol components
	Returns : Hash
	Args	: none

   iupac_rev_iub
	Title	: iupac_rev_iub
	Usage	: my %dnasymbols = $iupac->iupac_rev_iub
	Function: Returns a hash of nucleotide combinations -> IUPAC code
		  (a reverse of the iupac_iub hash).
	Returns : Hash
	Args	: none

   count
	Title	: count
	Usage	: my $total = $iupac->count();
	Function: Calculates the number of unique, unambiguous sequences that
		  this ambiguous sequence could generate
	Return	: int
	Args	: none

perl v5.14.2							    2012-03-02						    Bio::Tools::IUPAC(3pm)