Provided by: libbio-perl-perl_1.6.901-2_all bug

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