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OFRG
PRImer Selector(PRISE)
PRISE - PCR Primer Design Software

Brief Introduction

PRImer Selector (PRISE) is a software package that implements several features that improve and streamline the design of sequence-selective PCR primers. Although the motivation for its development was to facilitate examinations of microbial communities via rRNA gene analysis, we anticipate that it will be useful for any other application where sequence-selective PCR primers are needed.

The PRISE design process involves two main steps:

1.Target and non-target DNA sequences are identified.
2.Primers are designed to amplify target (but not non-target) sequences.

The most important feature of PRISE is its ability to place primer-template mismatches at the 3' end of the primers - a property that is crucial for sequence selectivity.

The software also provides sorting tools to:

1.Speed up the selection process by allowing a user to sort the primers by properties such as amplicon length, GC content and sequence selectivity.
2.Design primers with a range of specificities, targeting individual sequences as well as diverse assemblages of genes.
3.Allow user-defined primers to be analyzed, enabling their properties to be examined in relation to target and non-target sequences.

Publication

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

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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