Bio::Tools::Signalp(3)User Contributed Perl DocumentatioBio::Tools::Signalp(3)NAMEBio::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:
http://bugzilla.open-bio.org/
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 v5.14.1 2011-07-22 Bio::Tools::Signalp(3)
