Bio::Tools::PSort::ModuleI - an interface class that all PSort modules should
use vars qw(@ISA);
@ISA = qw(Bio::Tools::PSort::Module;
The module object contains functionality common to all PSort modules. This class
is not intended to be instantiated on it's own, it only provides functionality
common to all PSort modules.
$result = $module->run($seq);
The run method must be overridden in all derived classes. run()
accept a Bio::Tools::Seq object, and perform whatever analysis the module
provides on the sequence, returning a bio::PSort::Scort object upon
Bio::Tools::PSort, Bio::Tools::PSort::Pathway, Bio::Tools::PSort::Score
Fiona Brinkman, Cory Spencer <firstname.lastname@example.org>
Brinkman Laboratory, Simon Fraser University, BC, CANADA
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
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
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 email@example.com.
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
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