PSORTb version 3.0 README


Until the manuscript for PSORTb v.3.0 is released, if you use PSORTb in your research, please cite one of the following, noting the software version:

PSORTb v.2.0: J.L. Gardy, M.R. Laird, F. Chen, S. Rey, C.J. Walsh, M. Ester, and F.S.L. Brinkman (2005) PSORTb v.2.0: expanded prediction of bacterial protein subcellular localization and insights gained from comparative proteome analysis, Bioinformatics 21(5):617-623

PSORTb v.1.0: 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

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


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

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.


To install this package, please refer to the INSTALL file included with the distribution.


If you find a bug, please report it to along with the following information:

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!


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.


The modules distributed with the Bio::Tools::PSort package were originally written by Cory Spencer. There are currently maintained by the Brinkman Laboratory at Simon Fraser University, Burnaby, BC, Canada - Contact us at


Thanks go to all of the members of the SFU Brinkman Laboratory for being particularly helpful during the development process of this package.