PSORTb version 2.0.1 README -------------------------------------------------------------------------------------------- * OVERVIEW * DESCRIPTION * INSTALLATION * BUG REPORTING * COPYRIGHT AND LICENCE * AUTHOR INFORMATION * ACKNOWLEDGEMENTS -------------------------------------------------------------------------------------------- OVERVIEW PSORTb is described in: Gardy, J.L. et al (2003). PSORTb: improving protein subcellular localization prediction for Gram-negative bacteria. Nucleic Acids Research 31(13):3613-17. Please cite this publication if you use PSORTb in your research. The standalone version of PSORTb is distributed under the GNU General Public Licence (GNU GPL). The program was initially been developed for the Linux environment, but has since been ported to OS X (Darwin). This document describes the installation of the PSORTb version 2.0.1 command line program and the PSORTb server packages. For most purposes, following the installation instructions for the command line version will be sufficient - the server package installation instructions are only necessary if one wishes to set up their own local PSORTb server. For further information, please contact psort-mail@sfu.ca. -------------------------------------------------------------------------------------------- DESCRIPTION Computational prediction of the subcellular localization of proteins is a valuable tool for genome analysis and annotation, since a protein's subcellular localization can provide clues regarding its function in an organism. The Bio::Tools::PSort package implements a method for making such predictions. The original version of PSORT was developed by Kenta Nakai, at the Human Genome Center, Institute for Medical Science, University of Tokyo, Japan. The Brinkman Laboratory later headed development of PSORTb, an updated version of the PSORT algorithm designed for bacterial proteins. Bio::Tools::PSort and its associated modules were originally written by Cory Spencer of the Simon Fraser University Brinkman Laboratory. All inquiries, patches and comments should be sent to psort-mail@sfu.ca To read about the latest features, see the Changes file included in the downloadable PSORTb package. The author invites feedback on Bio::Tools::PSort. If you find a bug, please send the information described in the BUGS section below. -------------------------------------------------------------------------------------------- INSTALLATION To install this package, please refer to the INSTALL file included with the distribution. -------------------------------------------------------------------------------------------- BUG REPORTING If you find a bug, please report it to psort-mail@sfu.ca along with the following information: * version of Perl (output of 'perl -V' is best) * version of Bio::Tools::PSort * operating system type and version * exact text of error message or description of problem * example model files/data being classified If we don't have access to a system similar to yours, you may be asked to insert some debugging lines and report back on the results. The more help and information you can provide, the better! -------------------------------------------------------------------------------------------- COPYRIGHT AND LICENCE The modules distributed with Bio::Tools::PSort are Copyright (C) 2002 Cory Spencer and Fiona Brinkman. All rights reserved. This program is distributed under the GNU General Public License. See also the LICENCE file included with this package. -------------------------------------------------------------------------------------------- AUTHOR INFORMATION The modules distributed with the Bio::Tools::PSort package were originally written by Cory Spencer. They are currently maintained by the Brinkman Laboratory at Simon Fraser University, Burnaby, BC, Canada - http://www.brinkman.mbb.sfu.ca/ Contact us at psort-mail@sfu.ca -------------------------------------------------------------------------------------------- ACKNOWLEDGEMENTS Thanks go to all of the members of the SFU Brinkman Laboratory for being particularly helpful during the development process of this package.