- AUTHOR - Heikki Lehvaslaiho
Bio::SeqUtils - Additional methods for PrimarySeq objects
use Bio::SeqUtils; # get a Bio::PrimarySeqI compliant object, $seq, somehow $util = new Bio::SeqUtils; $polypeptide_3char = $util->seq3($seq); # or $polypeptide_3char = Bio::SeqUtils->seq3($seq); # set the sequence string (stored in one char code in the object) Bio::SeqUtils->seq3($seq, $polypeptide_3char); # translate a sequence in all six frames @seqs = Bio::SeqUtils->translate_6frames($seq);
This class is a holder of methods that work on Bio::PrimarySeqI- compliant sequence objects, e.g. Bio::PrimarySeq and Bio::Seq. These methods are not part of the Bio::PrimarySeqI interface and should in general not be 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. See Bio::PrimarySeqI, Bio::PrimarySeq, and Bio::Seq for more.
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 methods, seq3() and seq3in(), give out or read in protein sequences coded in three letter IUPAC amino acid codes.
The next two methods, translate_3frames() and translate_6frames(), wrap around the standard translate method to give back an array of three forward or all six frame translations.
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The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _
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. alphabet 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 sequence optional, defaults to '*' string used to separate the output amino acid codes, optional, defaults to ''
Title : seq3in Usage : $string = Bio::SeqUtils->seq3in($seq, 'MetGlyTer') Function: Method for in-place changing of the sequence of a Bio::PrimarySeqI sequence object. The three letter amino acid input string is converted into one letter code. Any unknown character triplet, including the default 'Xaa', is converted into 'X'. 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'
Title : translate_3frames Usage : @prots = Bio::SeqUtils->translate_3frames($seq) Function: Translate a nucleotide sequence in three forward frames. The IDs of the sequences are appended with '-0F', '-1F', '-2F'. Returns : An array of seq objects Args : sequence object same arguments as to Bio::PrimarySeqI::translate
Title : translate_6frames Usage : @prots = Bio::SeqUtils->translate_6frames($seq) Function: translate a nucleotide sequence in all six frames The IDs of the sequences are appended with '-0F', '-1F', '-2F', '-0R', '-1R', '-2R'. Returns : An array of seq objects Args : sequence object same arguments as to Bio::PrimarySeqI::translate
Title : valid_aa Usage : my @aa = $table->valid_aa Function: Retrieves a list of the valid amino acid codes Returns : array of all the valid amino acid codes Args : [optional] $code => [0 -> return list of 1 letter aa codes, 1 -> return list of 3 letter aa codes, 2 -> return associative array of both ]