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 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
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://www.bioperl.org/MailList.html - About the mailing lists

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.bioperl.org/bioperl-bugs/ 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 'type'

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