Provided by: libbio-perl-perl_1.7.2-2_all bug


       Bio::Tools::IUPAC - Generates unique sequence objects or regular expressions from an
       ambiguous IUPAC sequence


        use Bio::PrimarySeq;
        use Bio::Tools::IUPAC;

        # Get the IUPAC code for proteins
        my %iupac_prot = Bio::Tools::IUPAC->new->iupac_iup;

        # Create a sequence with degenerate residues
        my $ambiseq = Bio::PrimarySeq->new(-seq => 'ARTCGUTGN', -alphabet => 'dna');

        # Create all possible non-degenerate sequences
        my $iupac = Bio::Tools::IUPAC->new(-seq => $ambiseq);
        while ($uniqueseq = $iupac->next_seq()) {
            # process the unique Bio::Seq object.

        # Get a regular expression that matches all possible sequences
        my $regexp = $iupac->regexp();


       Bio::Tools::IUPAC is a tool that manipulates sequences with ambiguous residues following
       the IUPAC conventions. Non-standard characters have the meaning described below:

             Cornish-Bowden (1985) Nucl. Acids Res. 13: 3021-3030

           Symbol       Meaning      Nucleic Acid
            A            A           Adenine
            C            C           Cytosine
            G            G           Guanine
            T            T           Thymine
            U            U           Uracil
            M          A or C        aMino
            R          A or G        puRine
            W          A or T        Weak
            S          C or G        Strong
            Y          C or T        pYrimidine
            K          G or T        Keto
            V        A or C or G     not T (closest unused char after T)
            H        A or C or T     not G (closest unused char after G)
            D        A or G or T     not C (closest unused char after C)
            B        C or G or T     not A (closest unused char after A)
            X      G or A or T or C  Unknown (very rarely used)
            N      G or A or T or C  Unknown (commonly used)

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

           Symbol           Meaning
           A        Alanine
           B        Aspartic Acid, Asparagine
           C        Cysteine
           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

       There are a few things Bio::Tools::IUPAC can do for you:

       ·   report the IUPAC mapping between ambiguous and non-ambiguous residues

       ·   produce a stream of all possible corresponding unambiguous Bio::Seq objects given an
           ambiguous sequence object

       ·   convert an ambiguous sequence object to a corresponding regular expression


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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: Create a new IUPAC object, which acts as a sequence stream (akin to
        Args    : an ambiguously coded sequence object that has a specified 'alphabet'
        Returns : a Bio::Tools::IUPAC object.

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

        Title   : iupac
        Usage   : my %symbols = $iupac->iupac;
        Function: Returns a hash of symbols -> symbol components of the right type
                  for the given sequence, i.e. it is the same as iupac_iup() if
                  Bio::Tools::IUPAC was given a proteic sequence, or iupac_iub() if the
                  sequence was nucleic. For example, the key 'M' has the value ['A', 'C'].
        Args    : none
        Returns : Hash

        Title   : iupac_amb
        Usage   : my %symbols = $iupac->iupac_amb;
        Function: Same as iupac() but only contains a mapping between ambiguous residues
                  and the ambiguous residues they map to. For example, the key 'N' has
                  the value ['R', 'Y', 'K', 'M', 'S', 'W', 'B', 'D', 'H', 'V', 'N'],
                  i.e. it matches all other ambiguous residues.
        Args    : none
        Returns : Hash

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

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

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

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

        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).
        Args    : none
        Returns : Hash

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

        Title   : regexp
        Usage   : my $re = $iupac->regexp();
        Function: Converts the ambiguous sequence into a regular expression that
                  matches all of the corresponding ambiguous and non-ambiguous sequences.
                  You can further manipulate the resulting regular expression with the
                  Bio::Tools::SeqPattern module. After you are done building your
                  regular expression, you might want to compile it and make it case-
                     $re = qr/$re/i;
        Args    : 1 to match RNA: T and U characters will match interchangeably
        Return  : regular expression