Docs

1. How to select specific PCR primers with MFEprimer? This protocol firstly illustrates the thermodynamics process of primer binding and three core factors which can influence the nonspecific binding sites of a primer. Secondly, a step-by-step protocol was introduced to help users to choose the right parameters and run MFEprimer. Finally and importantly, We used an actual example to tell users how to read the MFEprimer results.

   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. (PDF)

2. The algorithm behind MFEprimer.

   Wubin Qu^#, Yang Zhou^#, Yanchun Zhang, Yiming Lu, Xiaolei Wang, Dongsheng Zhao, Yi Yang and Chenggang Zhang. MFEprimer-2.0: A fast thermodynamics-based program for checking PCR primer specificity. Nucleic Acids Res. 2012, 40 (W1): W205-W208. (PDF)

3. The first paper which describes MFEprimer.

   Wubin Qu, Zhiyong Shen, Dongsheng Zhao, Yi Yang and Chenggang Zhang. (2009) MFEprimer: multiple factor evaluation of the specificity of PCR primers. Bioinformatics, 25(2), 276-278. (PDF)