Tool:MFEprimer-2.0: A Fast Thermodynamics-Based Program For Checking Pcr Primer Specificity
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9.6 years ago
Wubin Qu ▴ 160

Evaluating the specificity of 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 mRNA/cDNA 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/.

pcr primer Tool • 5.4k views
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it does work perfectly! How excellent!

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Please use the new server: http://www.mfeprimer.com/

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7.5 years ago
Aaron H ▴ 170

Webserver seems to be dead

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That's the link problem. I updated the link address. Thanks.

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6.2 years ago

Been using MPprimer a lot in the past few months but cant' access it any more. Anything wrong?

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For MFEprimer, try http://mfeprimer.com/.

For MPprimer, I need more time.

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This already helps a lot, thanks!!!

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The server crashed and I am trying to solve this problem.

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