PSORT-B version 1.1.4 README TABLE OF CONTENTS OVERVIEW DESCRIPTION INSTALLATION BUG REPORTING COPYRIGHT AND LICENCE AUTHOR INFORMATION ACKNOWLEDGEMENTS 1) 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 gives an overview of the PSORT-B package you have downloaded. For installation instructions, please read the INSTALL file included with the package. For further information, please contact psort-mail@sfu.ca. 2) 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 headed development of PSORT-B, an updated version of the PSORT algorithm designed for Gram-negative bacterial proteins. This version of the program, and the version implemented by this package, can be found in the following publication: Jennifer L. Gardy, Cory Spencer, Ke Wang, Martin Ester, Gabor E. Tusnady, Istvan Simon, Sujun Hua, Katalin deFays, Christophe Lambert, Kenta Nakai and Fiona S.L. Brinkman (2003) PSORT-B: improving protein subcellular localization prediction for Gram-negative bacteria, Nucleic Acids Research 31(13):3613-17 Please refer to http://www.psort.org for more information. Bio::Tools::PSort and its associated modules were originally written by Cory Spencer of the Simon Fraser University Brinkman Laboratory. The package is currently maintained by Matthew Laird and all inquiries, patches and comments should be sent to him. To read about the latest features, see the Changes file included in the downloadable version of PSORT-B. The author invites feedback on Bio::Tools::PSort. If you find a bug, please send the information described in the BUGS section below. 3) INSTALLATION To install this package, please refer to the INSTALL file included with the distribution. 4) BUG REPORTING If you find a bug, please report it to the author 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. 5) 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. Please see the included LICENSE file for details of what this entails. 6) AUTHOR INFORMATION The modules distributed with the Bio::Tools::PSort package were originally written by Cory Spencer , but are currently maintained by Matthew Laird of the Brinkman Laboratory at Simon Fraser University, Burnaby, BC, Canada: http://www.pathogenomics.sfu.ca/brinkman 7) ACKNOWLEDGEMENTS Thanks go to all of the members of the SFU Brinkman Laboratory for being particularly helpful during the development process of this package.