Bio::Tools::IUPAC - Generates unique Seq objects from an ambiguous Seq object use Bio::Seq; use Bio::Tools::IUPAC; my $ambiseq = new Bio::Seq (-seq => 'ARTCGUTGR', -alphabet => '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 IUPAC-IUB SYMBOLS FOR NUCLEOTIDE NOMENCLATURE: 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 IUPAC-IUP AMINO ACID SYMBOLS: Biochem J. 1984 Apr 15; 219(2): 345-373 Eur J Biochem. 1993 Apr 1; 213(1): 2

Mailing Lists
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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 email or the web: bioperl-bugs@bioperl.org http://www.bugzilla.bioperl.org/ Email amackey@virginia.edu The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _

new
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 'alphabet'

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

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

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