Provided by: libbio-perl-perl_1.7.2-3_all bug

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:

         https://github.com/bioperl/bioperl-live/issues

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.