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

NAME

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

SYNOPSIS

        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();

DESCRIPTION

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

           IUPAC-IUB SYMBOLS FOR NUCLEOTIDE (DNA OR RNA) NOMENCLATURE:
             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)

           IUPAC-IUP AMINO ACID SYMBOLS:
             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

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

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

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

   iupac
        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

   iupac_amb
        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

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

   iupac_iup_amb
        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

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

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

   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).
        Args    : none
        Returns : Hash

   count
        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

   regexp
        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-
                  insensitive:
                     $re = qr/$re/i;
        Args    : 1 to match RNA: T and U characters will match interchangeably
        Return  : regular expression