---
name: "Bio::Tools::Motif"
section: "3pm"
platform: "linux"
package: "psortb"
version: "3.0.6+dfsg-4+b2"
release: "Debian 13 (Trixie)"
platforms: ["linux"]
url: "https://new.carta.tech/Bio::Tools::Motif"
---

# Bio::Tools::Motif(3pm)

Perl implementation of the Motif protein subcellular localization method.

## 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.