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.\" ========================================================================
.\"
.IX Title "Bio::Tools::IUPAC 3pm"
.TH Bio::Tools::IUPAC 3pm "2012-03-02" "perl v5.14.2" "User Contributed Perl Documentation"
.\" For nroff, turn off justification.  Always turn off hyphenation; it makes
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.SH "NAME"
Bio::Tools::IUPAC \- Generates unique Seq objects from an ambiguous Seq object
.SH "SYNOPSIS"
.IX Header "SYNOPSIS"
.Vb 2
\& use Bio::Seq;
\& use Bio::Tools::IUPAC;
\&
\& my $ambiseq = Bio::Seq\->new(\-seq => \*(AqARTCGUTGR\*(Aq, \-alphabet => \*(Aqdna\*(Aq);
\& my $stream  = Bio::Tools::IUPAC\->new(\-seq => $ambiseq);
\&
\& while ($uniqueseq = $stream\->next_seq()) {
\&     # process the unique Seq object.
\& }
.Ve
.SH "DESCRIPTION"
.IX Header "DESCRIPTION"
\&\s-1IUPAC\s0 is a tool that produces a stream of unique, \*(L"strict\*(R"\-satisfying Seq
objects from an ambiquous Seq object (containing non-standard characters given
the meaning shown below)
.PP
.Vb 10
\&        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.
.Ve
.PP
\&\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-
.PP
.Vb 10
\&       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
.Ve
.SH "FEEDBACK"
.IX Header "FEEDBACK"
.SS "Mailing Lists"
.IX Subsection "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.
.PP
.Vb 2
\&  bioperl\-l@bioperl.org                  \- General discussion
\&  http://bioperl.org/wiki/Mailing_lists  \- About the mailing lists
.Ve
.SS "Support"
.IX Subsection "Support"
Please direct usage questions or support issues to the mailing list:
.PP
\&\fIbioperl\-l@bioperl.org\fR
.PP
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.
.SS "Reporting Bugs"
.IX Subsection "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:
.PP
.Vb 1
\&  https://redmine.open\-bio.org/projects/bioperl/
.Ve
.SH "AUTHOR \- Aaron Mackey"
.IX Header "AUTHOR - Aaron Mackey"
Email amackey\-at\-virginia.edu
.SH "APPENDIX"
.IX Header "APPENDIX"
The rest of the documentation details each of the object
methods. Internal methods are usually preceded with a _
.SS "new"
.IX Subsection "new"
.Vb 6
\& 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 \*(Aqalphabet\*(Aq
.Ve
.SS "next_seq"
.IX Subsection "next_seq"
.Vb 5
\& Title   : next_seq
\& Usage   : $iupac\->next_seq()
\& Function: returns the next unique Seq object
\& Returns : a Seq.pm object
\& Args    : none.
.Ve
.SS "iupac_iup"
.IX Subsection "iupac_iup"
.Vb 5
\& Title   : iupac_iup
\& Usage   : my %aasymbols = $iupac\->iupac_iup
\& Function: Returns a hash of PROTEIN symbols \-> symbol components
\& Returns : Hash
\& Args    : none
.Ve
.SS "iupac_iub"
.IX Subsection "iupac_iub"
.Vb 5
\& Title   : iupac_iub
\& Usage   : my %dnasymbols = $iupac\->iupac_iub
\& Function: Returns a hash of DNA symbols \-> symbol components
\& Returns : Hash
\& Args    : none
.Ve
.SS "iupac_rev_iub"
.IX Subsection "iupac_rev_iub"
.Vb 6
\& 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
.Ve
.SS "count"
.IX Subsection "count"
.Vb 6
\& 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
.Ve