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.\" ========================================================================
.\"
.IX Title "Bio::Tools::Motif 3pm"
.TH Bio::Tools::Motif 3pm "2018-11-01" "perl v5.28.0" "User Contributed Perl Documentation"
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.SH "NAME"
Bio::Tools::Motif \- Perl implementation of the Motif protein subcellular
localization method.
.SH "SYNOPSIS"
.IX Header "SYNOPSIS"
.Vb 1
\&  use Bio::Tools::Motif;
\&
\&  # Load a previously trained model from a file.
\&  $motif = new Bio::Tools::Motif(\-database => \*(Aqmotif\-db.txt\*(Aq);
\&
\&  # Attempt to match on a Bio::Seq object.
\&  @matches = $motif\->match($seq);
\&  print($seq\->display_id . ": matched " . $_\->motif_id . "\en") for(@matches);
\&
\&  # Save the database to a file.
\&  $motif\->save(\*(Aqmotif\-db.txt.new\*(Aq);
\&
\&  # Load a database from a file.
\&  $motif\->load(\*(Aqmotif\-db.txt.new\*(Aq);
\&
\&  # Add a new Bio::Tools::Motif::Pattern.
\&  $motif\->add_pattern($pattern);
.Ve
.SH "DESCRIPTION"
.IX Header "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.
.SH "CONSTRUCTOR"
.IX Header "CONSTRUCTOR"
.Vb 1
\&   $motif = new Bio::Tools::Motif(\-database => \*(Aqmotif\-db.txt\*(Aq);
.Ve
.PP
The Motif constructor accepts the name of an existing database file.
.SH "METHODS"
.IX Header "METHODS"
.Vb 1
\&   @matches = $motif\->match($seq);
.Ve
.PP
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.
.PP
.Vb 1
\&  $motif\->add_pattern($pattern)
.Ve
.PP
The add_pattern method adds another Bio::Tools::Motif::Pattern method
to the list of patterns used to match against sequences.
.PP
.Vb 1
\&  $motif\->save(\*(Aqmotif\-db.txt.new\*(Aq);
.Ve
.PP
Saves the currently loaded database to the specified file.  Returns true on
success, false on failure.
.PP
.Vb 1
\&  $motif\->load(\*(Aqmotif\-db.txt.new\*(Aq);
.Ve
.PP
Loads an existing database from file.  Returns true on success, false on
failure.
.PP
The database is a file containing a series of tab delimited fields.  The
fields (in order) are: the motif \s-1ID,\s0 the localization site, the perl
regular expression used to match the motif and an optional comment field.
.SH "AUTHOR"
.IX Header "AUTHOR"
Cory Spencer <cspencer@sfu.ca>
.SH "SEE ALSO"
.IX Header "SEE ALSO"
Bio::Tools::Motif::Pattern, Bio::Tools::Motif::Match
.SH "ACKNOWLEGEMENTS"
.IX Header "ACKNOWLEGEMENTS"
Thanks go out to Fiona Brinkman, Jennifer Gardy and the other members of the
Simon Fraser University Brinkman laboratory.