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Bioinformatics Advance Access originally published online on November 27, 2008
Bioinformatics 2009 25(2):276-278; doi:10.1093/bioinformatics/btn614
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© The Author 2008. Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oxfordjournals.org

MFEprimer: multiple factor evaluation of the specificity of PCR primers

Wubin Qu 1,2, Zhiyong Shen 1, Dongsheng Zhao 3, Yi Yang 2,* and Chenggang Zhang 1,*

1Beijing Institute of Radiation Medicine, State Key Laboratory of Proteomics, Beijing 100850, 2College of Life Science, Sichuan University, Key Laboratory of Bio-Resources and Eco-Environment of MOE, Chengdu 610064 and 3Beijing Institute of Health Service and Medical Information, Beijing 100850, China

*To whom correspondence should be addressed.


  Abstract

Summary: We developed a program named MFEprimer for evaluating the specificity of PCR primers based on multiple factors, including sequence similarity, stability at the 3 ' -end of the primer, melting temperature, GC content and number of binding sites between the primer and DNA templates. MFEprimer can help the user to select more suitable primers before running either standard or multiplex PCR reactions. The cDNA and genomic DNA databases of 10 widely used species, as well as user custom databases, were used as DNA templates for analyzing primers specificity. Furthermore, we maintained a Primer3Plus server with a modified Primer3Manager for one-stop primer design and specificity checking.

Availability: The web service of MFEprimer is freely available at http://biocompute.bmi.ac.cn/MFEprimer/. A stand-alone version of MFEprimer can be downloaded at http://biocompute.bmi.ac.cn/MFEprimer/download/. Primer3Plus on our server is located at http://biocompute.bmi.ac.cn/MFEprimer/primer3plus.cgi. All programs are licensed under the General Public License (Free Software Foundation, 1991).

Contact: zhangcg{at}bmi.ac.cn

Supplementary information: Supplementary data are available at Bioinformatics online.

Associate Editor: David Rocke

Received on August 17, 2008; revised on October 26, 2008; accepted on November 23, 2008

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