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OFRG
PRImer Selector 2(PRISE2)
PRISE2 - PCR Primer Design Software

General Information


PRISE2 (PRImer Selector2) is a software package, developed at UC Riverside, that streamlines the design of sequence-selective PCR primers and probes. It was originally developed to facilitate examinations of microbial communities via rRNA gene analysis, but it is designed to be useful for any other application where sequence-selective PCR primers are needed. PRISE2 includes an intuitive and easy to use graphical interface, is easy to install, and runs on windows, macintosh and linux machines.

The design process in PRISE2 involves the following steps:

  1. First, target and non-target DNA sequences are identified by the user.
  2. Next, the program computes a collection of primers designed to amplify target (but not non-target) sequences.
  3. Finally, probes can be added to any selected pair of primers.

Features of PRISE2 include:

  • The ability to place primer-template mismatches at the 3' end of the primers - a property that is crucial for sequence selectivity.
  • A tool assisting the user in selecting target and non-target sequences.
  • Interactive tools for sorting the primers by properties such as primer length, GC content, product length, and sequence selectivity.
  • An option to manually add primers, which can then be analyzed, enabling their properties to be examined in relation to target and non-target sequences.
  • Similar tools for designing probes for selected primer pairs.


Contact Information


The PRISE2 development group consists of

  • Yu-Ting Huang, graduate student in Computer Science, nightfelidae@gmail.com,
  • Marek Chrobak, Professor of Computer Science, marek@cs.ucr.edu, and
  • James Borneman, Professor of Plant Pathology, borneman@ucr.edu.

Questions and comments regarding PRISE2 should be emailed to prise@cs.ucr.edu.


Publication / Documentation


  1. PRISE (PRImer SElector): Software for designing sequence-selective PCR primers. Qi Fu, Paul Ruegger, Elizabeth Bent, Marek Chrobak, James Borneman. Journal of Microbiological Methods. 2008 72(3): 263-267.
  2. PRISE2: Software for Designing Sequence-Selective PCR Primers and Probes. Yu-Ting Huang, Jiue-in Yang, Marek Chrobak, James Borneman. Manuscript under submission.
  3. PRISE2 Manual : Detailed instructions for using the software.
  4. PRISE2 Tutorial : An example showing, step-by-step, how the software can be used to design sequence-selective primers for an rRNA gene.
  5. PRISE2 FAQ (Frequently Asked Questions).


PRISE2 Download


Terms of Use: This software is available for free for non-commercial use. If you wish to use this software in a commercial setting, please contact the PRISE2 group for further information.

By downloading this software, you agree to the following conditions:

  • PRISE2 should not be used for commercial purposes, unless a special permission is secured.
  • Any publication resulting from work using PRISE2 should include a citation to the paper describing PRISE2 (see above).
  • PRISE2 is available "as is", with no explicit nor implied warranty.

PRISE2 requires a minimum of 512 MB of RAM (1 GB of RAM or more is recommended).
To download PRISE2, click on the link to the desired version. The package is a zip archive of a directory that contains all files needed for PRISE2's execution.

  • Download PRISE2 v1.2 - Windows version.
    System requirements: Windows 2000/NT/XP/7. To run PRISE2 on Windows system, extract prise2_win_v1.2.zip, go to the prise2_win_v1.2 directory, and then double click on PRISE2.exe.
  • Download PRISE2 v1.2 - Macintosh version.
    System requirements: Mac OS 10.5 or higher. To run PRISE2 on Macintosh system, extract prise2_mac_v1.2.zip, go to the prise2_mac_v1.2 directory,and then double click on PRISE2.run.

    Notice that for Mac 10.7 or higher, users may need to adjust the gatekeeper settings. The detail information is in PRISE FAQ and How to open apps from an unidentified developer in OS X Mountain Lion

  • Download PRISE2 v1.2 - Linux version.
    System requirements: Ubuntu 9.04 or higher. To run PRISE2 on Ubuntu system, extract prise2_ubuntu_v1.2.zip, go to the prise2_ubuntu_v1.2 directory, and then double click on PRISE2.


Old Version (PRISE)


PRISE2 is an extension of its previous version, PRISE. PRISE runs only on Windows, is slower than PRISE2, and it has more limited features (no option to design probes, for example). Although still available (through this link), it is not maintained anymore, and thus the users are recommended to upgrade it to Window version of PRISE2 instead.
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Copyright @ by Oligonucleotide Fingerprinting of Ribosomal RNA Genes(OFRG) Group (zliu@cs.ucr.edu, qfu@cs.ucr.edu), 2002

Last Modified on 04/25/2013