The name “MFEprimer” comes from the title of the first paper (2009, Bioinformatics): Multiple Factor Evaluation of the specificity of PCR primers. And both the version 1.0 and version 2.0 are only focused on primer specificity, leaving dimers and hairpins for users. However, dimers and hairpins are very important factors affecting success of PCR. So, for version 3.0, we expand the functions of MFEprimer, and make it as a full-functional primer quality control (PrimerQC, maybe the new name) program.

What is New?

  • Genomewide specificity evaluation. Mismatches at the 3’ end are allowed except the first base at the 3’ end. This feature will make the MFEprimer more sensitive and accurate, the cost is the need for more computing resources.
  • New and fast dimer evaluation algorithm;
  • New and fast hairpin evaluation algorithm;
  • Primers compatible evaluation for multiplex PCR;
  • Thermodynamics based hybridization stability analysis;
  • In addition to comprehensive background databases, custom databases are also supported upon request.

Online servers

  • MFEprimer-3.0 1# server hosted by iGeneTech: faster and mostly used background databases supported.
  • [available soon] MFEprimer-3.0 2# server hosted by Xiaolei Wang and Dr. Dongsheng Zhao: comprehensive background databases supported, but with a short time delay.

How to cite us

If you find MFEprimer useful, please consider citing this web site or the latest publication:

  • Wubin Qu. MFEprimer: PCR primer quality control for specificity, hairpins and dimers.
  • Wubin Qu and Chenggang Zhang. Selecting Specific PCR Primers with MFEprimer. In PCR Primer Design, edited by Chhandak Basu, 1275, 201-213: Springer New York, 2015.