Command-line PSORTb:

A command-line version of PSORTb for Linux and Mac OSX is available for download under the GNU General Public Licence (GNU GPL). If you make use of the program in your research, please cite either:

• PSORTb v.2.0: J.L. Gardy, M.R. Laird, F. Chen, S. Rey, C.J. Walsh, M. Ester, and F.S.L. Brinkman (2004) PSORTb v.2.0: expanded prediction of bacterial protein subcellular localization and insights gained from comparative proteome analysis, Bioinformatics (advance access) doi:10.1093/bioinformatics/bti057

• 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 PSORTb executables can be found beneath the following short survey...

Download the latest version of PSORTb for local use:

1. PSORTb module:

Bio-Tools-PSort-2.1.1 was released to address an incompatibility between Bioperl 1.6.0 and the PSORTb SCLBLAST module. This fix is backwards compatible with older versions of Bioperl. Released 2nd April 2009.

2. Required prerequisite modules:

These modules MUST be installed BEFORE PSORTb is installed.

• Bio-Tools-PSort-ModHMM
• Algorithm::SVM (view the SVMREADME file)
• Algorithm::HMM

You must also have the following components in place before PSORTb is installed.

• Either a Linux distribution or Mac OS X - PSORTb has been tested and found to work on the following Linux distributions to date: RedHat 7.3 and 9.0, SuSE 9.0, Mandrake 9.2.
• Perl version 5.005_03 or higher (5.6.x or higher recommended) - The latest version of Perl can be obtained from http://www.cpan.org
• The Bioperl library version 1.2.x or higher - While PSORTb *has* been tested on earlier versions of Bioperl, the latest version is strongly recommended. Bioperl can be obtained from http://www.bioperl.org
• A working installation of standalone NCBI BLAST - BLAST can be obtained from the NCBI FTP site at ftp://ftp.ncbi.nih.gov/blast/executables/
• A working installation of PFTOOLS - PFTOOLS can be obtained from http://www.isrec.isb-sib.ch/ftp-server/pftools/pft2.3/ or from our website
• A working version of the RPC::XML perl module version 1.26 or higher - XML::RPC can be obtained from http://www.cpan.org

Read the PSORTb instructions:

• README.html or README.txt
• INSTALL.html or INSTALL.txt
• Read the PSORTb User's Guide

Archives of previous versions of PSORTb can be found here.

Compatibility Notice: At this time, PSORTb will only function under Linux/x86, Linux(Opteron) and Mac OSX. If any researcher is able to patch PSORTb to operate under an operating system other than Linux, we would appreciate your description of the changes you made. Please contact us.