Provided by: libbio-perl-perl_1.7.2-2_all bug


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


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

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


       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


       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

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

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


             # if you want  meta sequences as well :
             my $meta = $tool->result('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::SimpleAnalysisI, Bio::Tools::Analysis::SimpleAnalysisBase, Bio::Seq::Meta::Array,


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

        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:

          Returns the raw ASCII data stream but without HTML tags

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

          Array of array references of [score, rank].

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