plucky (3) Bio::Tools::PSort.3pm.gz

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