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 :