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.\" ========================================================================
.\"
.IX Title "Bio::Tools::PSort::Profile 3pm"
.TH Bio::Tools::PSort::Profile 3pm "2018-11-01" "perl v5.28.0" "User Contributed Perl Documentation"
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.SH "NAME"
Bio::Tools::PSort::Profile \- Perl implementation of the Profile protein subcellular
localization method.
.SH "SYNOPSIS"
.IX Header "SYNOPSIS"
.Vb 1
\&  use Bio::Tools::PSort::Profile;
\&
\&  # Load a previously trained profile from a file.
\&  $motif = new Bio::Tools::PSort::Profile(\-database => \*(Aqprofile\-db.txt\*(Aq);
\&
\&  # Attempt to match on a Bio::Seq object.
\&  @matches = $motif\->match($seq);
\&  print($seq\->display_id . ": matched " . $_\->profile_id . "\en") for(@matches);
.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.
.SH "AUTHOR"
.IX Header "AUTHOR"
Fiona Brinkman, Chris Walsh, Matthew Laird <psort\-mail@sfu.ca>
Brinkman Lab, Simon Fraser University, Canada
.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.
.SH "POD ERRORS"
.IX Header "POD ERRORS"
Hey! \fBThe above document had some coding errors, which are explained below:\fR
.IP "Around line 99:" 4
.IX Item "Around line 99:"
=pod directives shouldn't be over one line long!  Ignoring all 2 lines of content