Ewan Birney


IUPAC - Generates unique Seq objects from an ambiguous Seq object


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

 my $ambiseq = new Bio::Seq (-seq => 'ARTCGUTGR', -type => 'Dna');
 my $stream  = new Bio::Tools::IUPAC(-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
        K        Lysine
        L        Leucine
        M        Methionine
        N        Asparagine
        P        Proline
        Q        Glutamine
        R        Arginine
        S        Serine
        T        Threonine
        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

Email amackey@virginia.edu


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


 Title   : new
 Usage   : new Bio::Tools::IUPAC $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 'type'


 Title   : next_seq
 Usage   : $iupac->next_seq()
 Function: returns the next unique Seq object
 Returns : a Seq.pm 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