PRImer Selector (PRISE) is an interactive software package for PCR primer design. PRISE enables the design of sequence-specific / sequence-selective PCR primers. One important feature of PRISE is that it automates the task of placing primer-template mismatches at the 3' end of the primers - a property that is crucial for sequence selectivity / specificity. PRISE was designed and developed by researchers and graduate students involved in the OFRG project. We stress, however, that PRISE is a generally applicable primer-design tool, not specific to its application in OFRG.
The PRISE design process involves two main steps. In the first step, target and non-target DNA sequences are identified. In the second step, primers are designed to amplify target (but not non-target) sequences. Once a list of candidate primers has been produced, sorting tools in PRISE speed up the selection process by allowing a user to sort the primers by properties such as amplicon length, GC content and sequence selectivity. PRISE can be used to design primers with a range of specificities, targeting individual sequences as well as diverse assemblages of genes. PRISE also allows user-defined primers to be analyzed, enabling their properties to be examined in relation to target and non-target sequences. The utility of PRISE was validated by using it to design sequence-selective PCR primers for an rRNA gene from the fungus Pochonia chlamydosporia.

PRISE was designed and developed by researchers and graduate students involved in the OFRG project. We stress, however, that PRISE is a generally applicable primer-design tool, not specific to its application in OFRG.

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

To run PRISE, make sure that all files and folders extracted from this zip file are in the same folder, and then run PRISE.exe. The supported platform are Windows 2000/NT/XP.