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¶

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Around line 99:

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