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


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


        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.


       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

                 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

                 Biochem J. 1984 Apr 15; 219(2): 345-373
                 Eur J Biochem. 1993 Apr 1; 213(1): 2


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AUTHOR - Aaron Mackey



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

        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 object that has a specified 'alphabet'

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

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

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

        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

        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