Bio::SeqUtils - Additional methods for PrimarySeq objects # get a Bio::PrimarySeqI compliant object, $seq, somehow $util = new Bio::SeqUtils; $poplypeptide_3char = $util->seq3($seq); #or $poplypeptide_3char = Bio::SeqUtils->seq3($seq); #set the sequence string (stored in one char code in the object) Bio::SeqUtils->seq3($seq, $poplypeptide_3char); This class is a holder of methods that work on the Bio::PrimarySeqI manpage compliant sequence objects, e.g. the Bio::PrimarySeq manpage and the Bio::Seq manpage. These methods are not part of the the Bio::PrimarySeqI manpage interface and should in general not essential to the primary function of sequence objects. If you are thinking of adding essential functions, it might be better to create your own sequence class. The methods take as their first argument a sequence object. It is possible to use methods without first creating a SeqUtils object, i.e. use it as an anonymous hash. The first two methodsgive out or read in protein sequences coded in three letter IUPAC amino acid codes.

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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@bio.perl.org http://bio.perl.org/bioperl-bugs/ Email: heikki@ebi.ac.uk Address: EMBL Outstation, European Bioinformatics Institute Wellcome Trust Genome Campus, Hinxton Cambs. CB10 1SD, United Kingdom The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _

seq3
Title : seq3 Usage : $string = Bio::SeqUtils->seq3($seq) Function: Read only method that returns the amino acid sequence as a string of three letter codes. moltype has to be 'protein'. Output follows the IUPAC standard plus 'Ter' for terminator. Any unknown character, including the default unknown character 'X', is changed into 'Xaa'. A noncoded aminoacid selenocystein is recognized (Sel, U). Returns : A scalar Args : character used for stop in the protein seqence optional, defaults to '*' string used to separate the output amino acid codes, optional, defaults to ''

seq3in
Title : seq3in Usage : $string = Bio::SeqUtils->seq3in($seq, 'MetGlyTer') Function: Read only method that returns the amino acid sequence as a string of three letter codes. moltype has to be 'protein'. Output follows the IUPAC standard plus 'Ter' for terminator. Any unknown character, including the default unknown character 'X', is changed into 'Xaa' Returns : Bio::PrimarySeq object; Args : character to be used for stop in the protein seqence, optional, defaults to '*' character to be used for unknown in the protein seqence, optional, defaults to 'X' string used to separate the output amino acid codes, optional, defaults to ''