debian man page for bio::tools::signalp

Bio::Tools::Signalp(3pm)				User Contributed Perl Documentation				  Bio::Tools::Signalp(3pm)

NAME
       Bio::Tools::Signalp - parser for Signalp output

SYNOPSIS
	use Bio::Tools::Signalp;

	my $parser = Bio::Tools::Signalp->new(-fh =>$filehandle );

	while( my $sp_feat = $parser->next_result ) {
	  if ($sp_feat->score > 0.9) {
	     push @likely_sigpep, $sp_feat;
	  }
	}

DESCRIPTION
       "SignalP" predicts the presence and location of signal peptide cleavage sites in amino acid sequences.

       Bio::Tools::Signalp parses the output of "SignalP" to provide a Bio::SeqFeature::Generic object describing the signal peptide found, if
       any. It returns a variety of tags extracted from the NN and HMM analysis. Most importantly, the "score()" attribute contains the NN
       probability of this being a true signal peptide.

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
	the Bioperl mailing list.  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 of the bugs and their resolution. Bug reports can be submitted va the
       web:

	 https://redmine.open-bio.org/projects/bioperl/

AUTHOR
       # Please direct questions and support issues to bioperl-l@bioperl.org

       Based on the EnsEMBL module Bio::EnsEMBL::Pipeline::Runnable::Protein::Signalp originally written by Marc Sohrmann (ms2_AT_sanger.ac.uk).
       Written in BioPipe by Balamurugan Kumarasamy savikalpa_AT_fugu-sg.org. Cared for by the Fugu Informatics team (fuguteam_AT_fugu-sg.org)

CONTRIBUTORS
       Torsten Seemann - torsten.seemann AT infotech.monash.edu.au

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

   new
	Title	: new
	Usage	: my $obj = Bio::Tools::Signalp->new();
	Function: Builds a new Bio::Tools::Signalp object
	Returns : Bio::Tools::Signalp
	Args	: -fh/-file => $val, # for initing input, see Bio::Root::IO

   next_result
	Title	: next_result
	Usage	: my $feat = $signalp->next_result
	Function: Get the next result set from parser data
	Returns : Bio::SeqFeature::Generic
	Args	: none

   _parse_hmm_result
	Title	: _parse_hmm_result
	Usage	: $self->_parse_hmm_result(\%feature)
	Function: Internal (not to be used directly)
	Returns : hash of feature values
	Args	: hash of more feature values

   _create_feature
	Title	: _create_feature
	Usage	: $self->create_feature(\%feature)
	Function: Internal (not to be used directly)
	Returns : hash of feature values
	Args	: hash of more feature values

   _seqname
	Title	: _seqname
	Usage	: $self->_seqname($name)
	Function: Internal (not to be used directly)
	Returns :
	Args	:

   _fact1
	Title	: _fact1
	Usage	: $self->fact1($fact1)
	Function: Internal (not to be used directly)
	Returns :
	Args	:

perl v5.14.2							    2012-03-02						  Bio::Tools::Signalp(3pm)