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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 one of the following, noting the version of the software:

  • PSORTb v.3.0: N.Y. Yu, J.R. Wagner, M.R. Laird, G. Melli, S. Rey, R. Lo, P. Dao, S.C. Sahinalp, M. Ester, L.J. Foster, and F.S.L. Brinkman (2010) PSORTb 3.0: improved protein subcellular localization prediction with refined localization subcategories and predictive capabilities for all prokaryotes. Bioinformatics 26(13):1608-1615.
  • 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. 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...

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Download the latest version of PSORTb for local use:

1. PSORTb module:

2. Required prerequisite modules:

These modules MUST be installed BEFORE PSORTb is installed.

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: Ubuntu.
  • 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

Read the PSORTb instructions:

Archives of previous versions of PSORTb can be found here.


Compatibility Notice: At this time, PSORTb will only function under Linux/x86, Linux 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.

 
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