Bio::Tools::Analysis::Protein::Domcut man page on Pidora

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Bio::Tools::Analysis::UsereContributedBio::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.

perl v5.14.1			  2011Bio::Tools::Analysis::Protein::Domcut(3)
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