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PSORTb version 3.0.5 README
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* OVERVIEW
* DESCRIPTION
* INSTALLATION
* BUG REPORTING
* COPYRIGHT AND LICENCE
* AUTHOR INFORMATION
* ACKNOWLEDGEMENTS
-----------------------------------------------------------------------------
OVERVIEW
PSORTb is described in: Gardy, J.L. et al (2003). PSORTb: improving
protein subcellular localization prediction for Gram-negative bacteria.
Nucleic Acids Research 31(13):3613-17. Please cite this publication if you
use PSORTb in your research.
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 (10.4 Darwin, NOT any
newer versions) and Solaris SPARC and x86.
This document describes the installation of the PSORTb version 3.0.0
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.
Two files have been updated in this latest version of the package. The
Gram positive and Gram negative bacterial BLAST databases have had 32 extra
sequences added, to improve predictions of more diverse species, in keeping
with the 2016 publication of the PSORTdb paper: Peabody MA, Laird MR,
Vlasschaert C, Lo R, Brinkman FS. (2016) PSORTdb: expanding the bacteria and
archaea protein subcellular localization database to better reflect
diversity in cell envelope structures. Nucleic Acids Research. 44(D1):D663-8.
For further information, please contact psort-mail@sfu.ca.
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DESCRIPTION
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. The
package is currently maintained by Matthew Laird and all inquiries,
patches and comments should be sent to him at lairdm@sfu.ca.
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.
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INSTALLATION
To install this package, please refer to the INSTALL file included with
the distribution.
-----------------------------------------------------------------------------
BUG REPORTING
If you find a bug, please report it to psort-mail@sfu.ca along with the
following information:
* version of Perl (output of 'perl -V' is best)
* version of Bio::Tools::PSort
* operating system type and version
* exact text of error message or description of problem
* example model files/data being classified
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!
-----------------------------------------------------------------------------
COPYRIGHT AND LICENCE
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.
-----------------------------------------------------------------------------
AUTHOR INFORMATION
The modules distributed with the Bio::Tools::PSort package were originally
written by Cory Spencer, but are currently maintained by Matthew Laird of
the Brinkman Laboratory at Simon Fraser University, Burnaby, BC, Canada -
http://www.pathogenomics.sfu.ca/brinkman
-----------------------------------------------------------------------------
ACKNOWLEDGEMENTS
Thanks go to all of the members of the SFU Brinkman Laboratory for being
particularly helpful during the development process of this package.
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