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

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

perl v5.34.0                                       2022-02-06                             Bio::Tools::Motif(3pm)

       Cory Spencer <cspencer@sfu.ca>

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

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

       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.

          @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.

         $motif->add_pattern($pattern)

       The add_pattern method adds another Bio::Tools::Motif::Pattern method to the list of patterns used to
       match against sequences.

         $motif->save('motif-db.txt.new');

       Saves the currently loaded database to the specified file.  Returns true on success, false on failure.

         $motif->load('motif-db.txt.new');

       Loads an existing database from file.  Returns true on success, false on failure.

       The database is a file containing a series of tab delimited fields.  The fields (in order) are: the motif
       ID, the localization site, the perl regular expression used to match the motif and an optional comment
       field.

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

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

         use Bio::Tools::Motif;

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

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

         # Save the database to a file.
         $motif->save('motif-db.txt.new');

         # Load a database from a file.
         $motif->load('motif-db.txt.new');

         # Add a new Bio::Tools::Motif::Pattern.
         $motif->add_pattern($pattern);