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