Command-line PSORT-B v.1.1.4:

Important: This is not the current version of PSORT-B. PSORT-B v.2.0 can be downloaded from the PSORT-B Downloads page.

A Linux version of PSORT-B v.1.1.4 is available for download under the GNU General Public Licence (GNU GPL). If you make use of the program in your research, please cite:

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.

Download the source code:

• Bio-Tools-PSort-1.1.4 (the PSORT-B version 1.1.4 executable)
• Algorithm::SVM (a prerequisite module, must be installed prior to installing PSORT-B, view the README file)
• Algorithm::HMM (a prerequisite module, must be installed prior to installing PSORT-B)

Installation instructions:

• INSTALL.txt (or view the HTML version)

Documentation:

• README.txt (or view the HTML version)
• User's Guide

Important note for users of RedHat9: There seem to be problems in RedHat 9 between Bioperl and BLAST, the system call to BLAST returns a -1 return code. Unfortunately despite our best efforts we can't solve this problem. As a result about 50% of the machines running RH9 which PSORT-B is installed onto won't run properly. We have only encountered problems with RH9 to date, and have successfully installed PSORT-B using the RedHat 7.3, SuSE 9.0, and Mandrake 9.2 distributions.

Should you wish to use a workaround we've developed you must comment out the line:
$self->throw("$executable call crashed: $? $commandstring\n") unless ($status==0) ;
in the file:
Bio/Tools/Run/StandAloneBlast.pm at approximately line 633.