MPRIMER is a reliable, flexible and high-throughput multiplex PCR primer design software. It i) utilizes the famous Primer3 program to select candidate primers; ii) uses thermodynamics to measure the stability of misprimer and dimers; iii) implements k-mer index algorithm to fast check the specificity against large genome database; iv) designs a flexible plugin mechanism for easily extending the applications; v) has a self-learning system to redesign primers when primers are incompatible; vi) can auto-group the incompatible templates into different tubes; vii) is suitable for high-throughput primer design.
CZlab @ Beijing Institute of Radiation Medcine
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Zhiyong Shen, Wubin Qu, Wen Wang, Yiming Lu, Yonghong Wu, Zhifeng Li, Xingyi Hang, Xiaolei Wang, Dongsheng Zhao, Chenggang Zhang.
MPprimer: a program for reliable multiplex PCR primer design.
BMC Bioinformatics, 2010, 11:143