Download, unpack and copy the easyPAC folder including all subdirectories to a desired location on your computer.
easyPAC will create output files and temporary files so you should have the administrative permission to write files
in this directory while running easyPAC.
We provide easyPAC as executable file (easyPAC.exe) that runs on Windows (64bit) systems without further requirements.
Nevertheless this executable file requires the files supplied within the easyPAC_files folder so do not separate the
executable file from this folder. easyPAC.exe is a large file and it may take several seconds until the easyPAC window
pops up after double clicking. Alternatively, we provide the original and platform independent Perl script containing
the easyPAC source code. Running easyPAC as Perl script requires the installation of a Perl interpreter which is part
of a freely available Perl distribution like
Strawberry Perl http://strawberryPerl.com/
or ActivePerl http://www.activestate.com/ActivePerl
Normally, Perl is preinstalled on Macintosh and Linux systems. However, the installation of additional Perl modules may
be required if they are not already part of the installed Perl distribution. Additional Perl modules are freely available
at the Comprehensive Perl Archive Network (CPAN, http://www.cpan.org/). In addition, we provide modules that normally are
not part of a standard Perl distribution in the easyPAC_files/CPAN_modules folder. See http://www.cpan.org/ for
installation instructions.
easyPAC optionally searches primer candidates in reference files via SeqMap (Jiang and Wong 2008). SeqMap
executables are provided within the easyPAC_files folder and easyPAC will automatically choose the right file for your
operating system (Windows, Linux or Macintosh OS). If you are on a different operating system, SeqMap search is not
supported. If you use SeqMap for primer search, please also cite the Jiang and Wong paper.
Please allways use the latest version of the easyPAC software. easyPAC is freely available at:
http://sourceforge.net/projects/easypac/
or
http://www.uni-mainz.de/FB/Biologie/Anthropologie/472_ENG_HTML.php
Update history:
01.05.2012 - Bug fixed: In special cases, primers that did match to a reference sequence were not rejected.
02.08.2012 - Bug fixed: Primers were rejected when they mapped to a gap despite allowing a defined number of gaps in alignment.
03.05.2013 - easyPAC includes 64bit Windows version of SeqMap. Colors in graphical output (annotation/conservation) changed.
Citation:
David Rosenkranz. easyPAC: A Tool for Fast Prediction, Testing and Reference Mapping of Degenerate PCR Primers from
Alignments or Consensus Sequences. Evolutionary Bioinformatics 2012:8 151-159
Contact:
rosenkrd@uni-mainz.de
