| Bio::Tools::Signalp(3pm) | User Contributed Perl Documentation | Bio::Tools::Signalp(3pm) |
Bio::Tools::Signalp - parser for Signalp output
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;
}
}
"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.
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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.
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# 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)
Torsten Seemann - torsten.seemann AT infotech.monash.edu.au
The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _
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
Title : next_result Usage : my $feat = $signalp->next_result Function: Get the next result set from parser data Returns : Bio::SeqFeature::Generic Args : none
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
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
Title : _seqname Usage : $self->_seqname($name) Function: Internal (not to be used directly) Returns : Args :
Title : _fact1 Usage : $self->fact1($fact1) Function: Internal (not to be used directly) Returns : Args :
| 2021-08-15 | perl v5.32.1 |