plucky (3) Bio::Tools::Signalp.3pm.gz

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    :