QuantPrime - a flexible tool for reliable high-throughput primer design for quantitative PCR

Background: Medium- to large-scale expression profiling using quantitative polymerase chain reaction (qPCR) assays are becoming increasingly important in genomics research. A major bottleneck in experiment preparation is the design of specific primer pairs, where researchers have to make several informed choices, often outside their area of expertise. Using currently available primer design tools, several interactive decisions have to be made, resulting in lengthy design processes with varying qualities of the assays. Results: Here we present QuantPrime, an intuitive and user-friendly, fully automated tool for primer pair design in small- to large-scale qPCR analyses. QuantPrime can be used online through the internet http://www.quantprime.de/ or on a local computer after download; it offers design and specificity checking with highly customizable parameters and is ready to use with many publicly available transcriptomes of important higher eukaryotic model organisms and plant crops (...

• Type: Journal
• Year: 2008
• Where: BMCBI
• Authors: Samuel Arvidsson, Miroslaw Kwasniewski, Diego Mauricio Riaño-Pachón, Bernd Mueller-Roeber
• Keywords: BMCBI 2007, BMCBI 2008, Design, Primer Design, Primer Pairs