A practical algorithm for multiplex PCR primer set selection

Authors:
Jingli Wu;Jianxin Wang;Jian'/er Chen
Affiliations:
School of Information Science and Engineering, Central South University Changsha, 410083, China/ Department of Computer Science, Guangxi Normal University Guilin, 541004, China.;School of Information Science and Engineering, Central South University Changsha, 410083, China.;School of Information Science and Engineering, Central South University Changsha, 410083, China/ Department of Computer Science, Texas A&M University College Station, TX 77843, USA
Venue:
International Journal of Bioinformatics Research and Applications
Year:
2009

Citing 5
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Abstract

Selecting the minimum primer set with multiple constraints is an effective method for a successful and economical Multiplex Polymerase Chain Reaction (MP-PCR) experiment. However, there is no suitable algorithm for solving the problem. In this paper, a mathematical model is presented for the minimum primer set selection problem with multiple constraints. By introducing a novel genetic operator, we developed a parthenogenetic algorithm MG-PGA to solve the model. Experimental results show that MG-PGA can not only find a small primer set, but can also satisfy multiple biological constraints. Therefore, MG-PGA is a practical solution for MP-PCR primer design.