MFEprimer-2.0: a fast thermodynamics-based program for checking PCR primer specificity.
Evaluating the specificity of polymerase chain reaction (PCR) primers is an essential step in PCR primer design. The MFEprimer-2.0 server allows users to check primer specificity against genomic DNA and messenger RNA/complementary DNA sequence databases quickly and easily. MFEprimer-2.0 uses a k-mer index algorithm to accelerate the search process for primer binding sites and uses thermodynamics to evaluate binding stability between each primer and its DNA template. Several important characteristics, such as the sequence, melting temperature and size of each amplicon, either specific or non-specific, are reported on the results page. Based on these characteristics and the user-friendly output, users can readily draw conclusions about the specificity of PCR primers. Analyses for degenerate primers and multiple PCR primers are also supported in MFEprimer-2.0. In addition, the databases supported by MFEprimer-2.0 are comprehensive, and custom databases can also be supported on request. The MFEprimer-2.0 server does not require a login and is freely available at http://biocompute.bmi.ac.cn/CZlab/MFEprimer-2.0. More over, the MFEprimer-2.0 command-line version and local server version are open source and can be downloaded at https://github.com/quwubin/MFEprimer/wiki/Manual/.
Beijing Institute of Radiation Medicine, State Key Laboratory of Proteomics, Cognitive and Mental Health Research Center, Beijing 100850, China.
Wubin
W
Qu
Yang
Y
Zhou
Yanchun
Y
Zhang
Yiming
Y
Lu
Xiaolei
X
Wang
Dongsheng
D
Zhao
Yi
Y
Yang
Chenggang
C
Zhang
D000465:Algorithms; D001665:Binding Sites; D004247:DNA / Q000737:chemistry; D017931:DNA Primers / Q000737:chemistry*; D020407:Internet; D016133:Polymerase Chain Reaction; D017422:Sequence Analysis, DNA; D012984:Software; D013698:Templates, Genetic; D013816:Thermodynamics
D017931:DNA Primers; D004247:DNA