plucky (3) Bio::Tools::PSort::Profile.3pm.gz

NAME

       Bio::Tools::PSort::Profile - Perl implementation of the Profile protein subcellular localization method.

SYNOPSIS

         use Bio::Tools::PSort::Profile;

         # Load a previously trained profile from a file.
         $motif = new Bio::Tools::PSort::Profile(-database => 'profile-db.txt');

         # Attempt to match on a Bio::Seq object.
         @matches = $motif->match($seq);
         print($seq->display_id . ": matched " . $_->profile_id . "\n") for(@matches);

DESCRIPTION

       Bio::Tools::Motif uses a selection of motifs that have been identified to be typical of proteins resident
       at a specific subcellular localization.  The module accepts a Bio::Seq object and attempts to match it
       against a database, returning one or more Bio::Tools::Motif::Match objects with the prediction
       information if successful.

CONSTRUCTOR

          $motif = new Bio::Tools::Motif(-database => 'motif-db.txt');

       The Motif constructor accepts the name of an existing database file.

METHODS

          @matches = $motif->match($seq);

       The match method accepts a Bio::Seq object as an argument and returns an array of
       Bio::Tools::Motif::Match objects that matched the given sequence.

AUTHOR

       Fiona Brinkman, Chris Walsh, Matthew Laird <psort-mail@sfu.ca> Brinkman Lab, Simon Fraser University,
       Canada

SEE ALSO

       Bio::Tools::Motif::Pattern, Bio::Tools::Motif::Match

ACKNOWLEGEMENTS

       Thanks go out to Fiona Brinkman, Jennifer Gardy and the other members of the Simon Fraser University
       Brinkman laboratory.

POD ERRORS

       Hey! The above document had some coding errors, which are explained below:

       Around line 99:
           =pod directives shouldn't be over one line long!  Ignoring all 2 lines of content