Bio::Tools::Analysis::Protein::Domcut(3)

NAME
Bio::Tools::Analysis::Protein::Domcut - a wrapper around Domcut server

SYNOPSIS
  use   Bio::Tools::Analysis::Protein::Domcut;
  #get a  Bio::PrimarySeq
  use Bio::PrimarySeq;
  my $seq = Bio::PrimarySeq->new
     (-seq=>'IKLCVNLAILAKAHLIELALAL',
     -primary_id=>'test'); # a Bio::PrimarySeqI object

  my $domcut = Bio::Tools::Analysis::Protein::Domcut->new (-seq=>$seq);
  $domcut->run;
  print $domcut->result;# #raw text to standard out

DESCRIPTION
A module to remotely retrieve predictions of protein domain boundaries. Each residue in the protein receives a score, those better than the significance threshold and at a local minimum receive a rank - i.e., the best minimum is rank 1, the second best minimum is rank2 etc. These correspond to domain boundaries. e.g.,

  my $analysis_object = Bio::Tools::Analysis::Protein::Domcut->new
     (-seq => $seq);

creates a new object. The sequence supplied must be a Bio::PrimarySeq and not a Bio::Seq object.

  $analysis_object->run;

submits the query to the server and obtains raw text output

Given an amino acid sequence the results can be obtained in 4 formats, determined by the argument to the result method

1.  The raw text of the program output

      my $rawdata = $analysis_object->result;

2.  A reference to an array of hashes of scores for each state and the assigned state. Each element in the array is a residue (indexed from 0).

      my $data_ref = $analysis_object->result('parsed');
      print "score for helix at residue 2 is $data_ref->[1]{'helix'}\n";
      print "predicted struc  at residue 2 is $data_ref->[1]{'struc}\n";

3.  An array of Bio::SeqFeature::Generic objects where each feature is a predicted unit of secondary structure. Only stretches of helix/sheet predictions for longer than 4 residues are defined as helices. So, in order to add features to an existing Bio::Seq object;

      # get a Bio::Seq object
      my $seqobj;
      my $tool = Bio::Tools::Analysis::Protein::Domcut->new
          ( -seq => $seqobj->primary_seq);
      $tool->run;

      my @fts = $tool->result(Bio::SeqFeatureI);

      $seqobj->add_SeqFeature(@fts);

      # if you want  meta sequences as well :
      my $meta = $tool->result('meta');
      $seqobj->primary_seq($meta);

      # can access meta data in a Bio::Seq object via a
      # call to primary_seq:

      print $seq4->primary_seq->named_submeta_text('Domcut', 1,2), "\n";

4.  A Bio::Seq::Meta::Array implementing sequence.

    This is a Bio::Seq object that can also hold data about each residue in the sequence. In this case, the sequence can be associated with a single array of Domcut prediction scores. e.g.,

      my $meta_sequence = $analysis_object->result('meta');
      print "scores from residues 10 -20 are ",
          $meta_sequence->submeta_text(10,20), "\n";

    Many methods common to all analyses are inherited from Bio::Tools::Analysis::SimpleAnalysisBase.

SEE ALSO
Bio::SimpleAnalysisI, Bio::Tools::Analysis::SimpleAnalysisBase, Bio::Seq::Meta::Array, Bio::WebAgent

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://bioperl.org/wiki/Mailing_lists  - About the mailing lists

  Support
Please direct usage questions or support issues to the mailing list:

bioperl-l@bioperl.org

rather than to the module maintainer directly. Many experienced and reponsive experts will be able look at the problem and quickly address it. Please include a thorough description of the problem with code and data examples if at all possible.

  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 the web:

  http://bugzilla.open-bio.org/

AUTHORS
Richard Adams, Richard.Adams@ed.ac.uk,

APPENDIX
The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _

  result
 Name    : result
 Purpose : To retrieve results of analysis in one of several formats.
 Usage   : $job->result (...)
 Returns : a result created by running an analysis
 Args    : various - see keysin $RESULT_SPEC.

The method returns a result of an executed job. If the job was terminated by an error the result may contain an error message instead of the real data.

This implementation returns differently processed data depending on argument:

undef
    Returns the raw ASCII data stream but without HTML tags

'Bio::SeqFeatureI'
    The argument string defines the type of bioperl objects returned in an array. The objects are Bio::SeqFeature::Generic. Tagnames are 'score' and 'rank'.

'parsed'
    Array of array references of [score, rank].

'all'
    A Bio::Seq::Meta::Array object. Scores can be accessed using methods from this class. Meta sequence name is Domcut.