NAME

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

SYNOPSIS

         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);

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.

         $motif->add_pattern($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.

AUTHOR

       Cory Spencer <cspencer@sfu.ca>

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.