/ 
bioperl-1.4
/ Bio::SeqUtils

NAME

Bio::SeqUtils - Additional methods for PrimarySeq objects

SYNOPSIS

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);

# inplace editing of the sequence
Bio::SeqUtils->mutate($seq,
                      Bio::LiveSeq::Mutation->new(-seq => 'c',
                                                  -pos => 3
                                                 ));

DESCRIPTION

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.

The last method mutates the sequence string.

FEEDBACK

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://bio.perl.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@bio.perl.org
http://bugzilla.bioperl.org/

AUTHOR - Heikki Lehvaslaiho

Email: heikki@ebi.ac.uk Address:

EMBL Outstation, European Bioinformatics Institute
Wellcome Trust Genome Campus, Hinxton
Cambs. CB10 1SD, United Kingdom

APPENDIX

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. 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 (Sec, 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 ''

seq3in

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'

translate_3frames

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

translate_6frames

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

valid_aa

 Title   : valid_aa
 Usage   : my @aa = $table->valid_aa
 Function: Retrieves a list of the valid amino acid codes.
           The list is ordered so that first 21 codes are for unique 
           amino acids. The rest are ['B', 'Z', 'X', '*'].
 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 ]

mutate

Title   : mutate
Usage   : Bio::SeqUtils->mutate($seq,$mutation1, $mutation2);
Function: 

          Inplace editing of the sequence.

          The second argument can be a Bio::LiveSeq::Mutation object
          or an array of them. The mutations are applied sequentially
          checking only that their position is within the current
          sequence.  Insertions are inserted before the given
          position.

Returns : boolean
Args    : sequence object
          mutation, a Bio::LiveSeq::Mutation object, or an array of them

See Bio::LiveSeq::Mutation.