pcrEfficiency: a Web tool for PCR amplification efficiency prediction

BMC Bioinformatics

Research Article

Izaskun Mallona¹  Julia Weiss¹  Marcos Egea-Cortines¹ 

[1] Genetics, Institute of Plant Biotechnology (IBV), Technical University of Cartagena (UPCT), Campus Muralla del Mar, 30202, Cartagena, Spain;

关键词: Amplification Efficiency;    Generalize Additive Model;    Common Gateway Interface;    Receiver Operator Characteristic Space;    Prostate Serum Antigen;   

DOI  :  10.1186/1471-2105-12-404

 received in 2011-05-12, accepted in 2011-10-20,  发布年份 2011

来源: Springer

【 摘 要 】

BackgroundRelative calculation of differential gene expression in quantitative PCR reactions requires comparison between amplification experiments that include reference genes and genes under study. Ignoring the differences between their efficiencies may lead to miscalculation of gene expression even with the same starting amount of template. Although there are several tools performing PCR primer design, there is no tool available that predicts PCR efficiency for a given amplicon and primer pair.ResultsWe have used a statistical approach based on 90 primer pair combinations amplifying templates from bacteria, yeast, plants and humans, ranging in size between 74 and 907 bp to identify the parameters that affect PCR efficiency. We developed a generalized additive model fitting the data and constructed an open source Web interface that allows the obtention of oligonucleotides optimized for PCR with predicted amplification efficiencies starting from a given sequence.ConclusionspcrEfficiency provides an easy-to-use web interface allowing the prediction of PCR efficiencies prior to web lab experiments thus easing quantitative real-time PCR set-up. A web-based service as well the source code are provided freely at http://srvgen.upct.es/efficiency.html under the GPL v2 license.

【 授权许可】

CC BY   
© Mallona et al; licensee BioMed Central Ltd. 2011