Skip site navigation (1)Skip section navigation (2)

FreeBSD Manual Pages

  
 
  

home | help
Bio::Tools::Signalp(3)User Contributed Perl DocumentatioBio::Tools::Signalp(3)

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

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 v5.32.1			  2019-12-07		Bio::Tools::Signalp(3)

NAME | SYNOPSIS | DESCRIPTION | FEEDBACK | AUTHOR | CONTRIBUTORS | APPENDIX

Want to link to this manual page? Use this URL:
<https://www.freebsd.org/cgi/man.cgi?query=Bio::Tools::Signalp&sektion=3&manpath=FreeBSD+13.0-RELEASE+and+Ports>

home | help