Bio::Tools::Signalp(3pm)

Usage

 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;
   }
 }

Overview

"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.
  [email protected]                  - General discussion
  http://bioperl.org/wiki/Mailing_lists  - About the mailing lists

Support

Please direct usage questions or support issues to the mailing list:

[email protected]

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

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    :

Releases

9 releases since Debian 5.0 (Lenny); the text changed 7 times.

5.0
6.0
7
8
9
10
11
12–13