Bio::Tools::Motif3pm

Usage

  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);

Overview

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.

Acknowlegements

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