title: PRISE (PRImer SElector): software for designing sequence-selective PCR primers.
abstract: This report presents PRImer Selector (PRISE), a new software package that implements several features that improve and streamline the design of sequence-selective PCR primers. 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. 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. 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 demonstrated by using it to design sequence-selective PCR primers for an rRNA gene from the fungus Pochonia chlamydosporia.
authors.affiliation: Department of Plant Pathology, University of California, Riverside, CA 92521, USA.
authors.forename: Qi
authors.initials: Q
authors.lastname: Fu
authors.forename: Paul
authors.initials: P
authors.lastname: Ruegger
authors.forename: Elizabeth
authors.initials: E
authors.lastname: Bent
authors.forename: Marek
authors.initials: M
authors.lastname: Chrobak
authors.forename: James
authors.initials: J
authors.lastname: Borneman
mesh_terms: D019295:Computational Biology / Q000379:methods*; D017931:DNA Primers / Q000235:genetics*; D004271:DNA, Fungal / Q000235:genetics; D004275:DNA, Ribosomal / Q000235:genetics; D006999:Hypocreales / Q000235:genetics; D016133:Polymerase Chain Reaction / Q000379:methods*; D012984:Software
chemical_list: D017931:DNA Primers; D004271:DNA, Fungal; D004275:DNA, Ribosomal