Archived versions of Command-line PSORTb:

Older versions of PSORTb (2.1.1 and earlier) can be found on this page. If you are looking for the latest version of PSORTb, please go to the main Downloads page.

Command-line versions of PSORTb for Linux and Mac OSX is available for download under the GNU General Public License (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 PSORTb executables:

1. Archived versions of 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.

Bio-Tools-PSort-2.1.0 is the first version of PSORTb which does not require an installed HMMTOP as prerequisite. The recall and precision of this version are comparable to the previous release of PSORTb. Released 20th April 2007.

Bio-Tools-PSort-All-2.0.6 is the seven release of PSORTb correcting a module naming conflict. It is operational under Linux, Mac OSX 10.3 and earlier, and Solaris and analyzes both Gram-negative and Gram-positive bacteria. Released 18th August 2005. (Gardy et al, 2004) We are currently working on fixing a bug with Mac OSX 10.4 installation.

Bio-Tools-PSort-2.0.4 fixes a bug supressing an HMMTOP warning message. It is operational under Linux, Mac OSX, and Solaris and analyzes both Gram-negative and Gram-positive bacteria. Released 8th March 2005. (Gardy et al, 2004)

Bio-Tools-PSort-2.0.3 is the fifth release of PSORTb. It is operational under Linux, Mac OSX, and Solaris and analyzes both Gram-negative and Gram-positive bacteria. Released 18th January 2005. (Gardy et al, 2004)

Bio-Tools-PSort-2.0.2 is the fourth release of PSORTb. It is operational under Linux, Mac OSX, and Solaris and analyzes both Gram-negative and Gram-positive bacteria. Developed 17th November 2004. (Gardy et al, 2004)

Bio-Tools-PSort-2.0.1 represents the third version (2.0.1) of the software. It is operational under Linux and Mac OSX. and analyzes both Gram-negative and Gram-positive bacteria. Developed 18th October 2004. (Gardy et al, 2004)

Bio-Tools-PSort-1.1.4 represents the second version (1.1.4) of the software. It is operational under Linux only, and is restricted to the analysis of Gram-negative bacteria. It contains a minor modification to report exact (100%) matches to proteins in the SCL-BLAST database. Developed 24th December 2003. (Gardy et al, 2003)

Bio-Tools-PSort-1.1.3 represents the first version (1.1.3) of the PSORTb software. It is operational under Linux only, and is restricted to the analysis of Gram-negative bacteria. Developed 9th July 2003. (Gardy et al, 2003)

2. Required prerequisite modules:

These modules MUST be installed BEFORE PSORTb is installed.

• 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 HMMTOP - HMMTOP can be obtained from http://www.enzim.hu/hmmtop/
• PFTOOLS - PFTOOLS can be downloaded from it's original source at https://github.com/sib-swiss/pftools3 or from our website
• A working version of the XML-RPC 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
• INSTALLv2.1.0.html or INSTALLv2.txt
• Read the PSORTb User's Guide

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 then these, we would appreciate your description of the changes you made. Please contact us.