NAME

       Bio::Tools::PSort - Module implementing a method for predicting protein localization
       sites.

SYNOPSIS

           $psort = new Bio::Tools::PSort();

           $psort->install('Motif', 'Motif', { -database => $motifdb });

           $psort->classify($seq);

DESCRIPTION

       The PSort module implements a method for predicting protein localization sites as dicussed
       in the paper 'Expert System for Predicting the Protein Localization Sites in Gram-Negative
       Bacteria' by Kenta Nakai and Minoru Kanehisa.

CONSTRUCTOR

           $psort = new Bio::Tools::PSort();

       Creates a new Bio::Tools::PSort object.

METHODS

           $psort->install('Motif', 'Motif', { -database => $motifdb });

       The install method can be used to load a module after the PSort class has been
       instantiated.  It accepts the name of the module to load, an alias used to refer to the
       module by the program, and an optional hashref of parameters that should be passed to the
       modules constructor.  The alias allows the same module to be loaded more than once, but
       with different configuration options.

           $result = $psort->classify($seq);

       The clasif method attempts to determine the likely protein localization for the provided
       sequence.  A Bio::Tools::PSort::Report object is returned.

SEE ALSO

       Bio::Tools::PSort::ModuleI, Bio::Tools::PSort::Score, Bio::Tools::PSort::Report,
       Bio::Tools::PSort::Report::Formatter

AUTHOR

        Fiona Brinkman, Cory Spencer <psort-mail@sfu.ca>
        Brinkman Laboratory, Simon Fraser University, BC, Canada

MAINTAINER

        Matthew Laird <lairdm@sfu.ca>
        Brinkman Laboratory, Simon Fraser University, BC, Canada

OVERVIEW

       PSORT-B is described in Gardy, J.L. et al (2003). PSORT-B: improving protein subcellular
       localization prediction for Gram-negative bacteria. Nuc Acids Res 31(13):3613-17. Please
       cite this publication if you use PSORT-B in your research.

       The standalone version of PSORT-B is distributed under the GNU General Public Licence (Gnu
       GPL) (see the LICENSE file included in the download) by the Brinkman Laboratory, Simon
       Fraser University, Burnaby, B.C., Canada.

       This standalone version of PSORT-B has initially been developed for the Linux environment.

       This document describes the installation of the PSORT-B version 1.1.4 command line program
       and the PSORT-B server packages. For most purposes, following the installation
       instructions for the command line version will be sufficient.

       For further information, please contact psort-mail@sfu.ca.

LICENSE

       This program is free software; you can redistribute it and/or modify it under the terms of
       the GNU General Public License as published by the Free Software Foundation; either
       version 2 of the License, or (at your option) any later version.

       This program is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY;
       without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.
       See the GNU General Public License for more details.

       You should have received a copy of the GNU General Public License along with this program;
       if not, write to the Free Software Foundation, Inc., 59 Temple Place, Suite 330, Boston,
       MA  02111-1307  USA