Title: A practical algorithm for multiplex PCR primer set selection

Authors: Jingli Wu, Jianxin Wang, Jian'er Chen

Addresses: 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

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.

Keywords: MP-PCR; multiplex polymerase chain reaction; primer set selection; primer design; greedy algorithms; parthenogenetic algorithms; genetic operator; DNA sequences; biological constraints; bioinformatics.

DOI: 10.1504/IJBRA.2009.022462

International Journal of Bioinformatics Research and Applications, 2009 Vol.5 No.1, pp.38 - 49

Published online: 07 Jan 2009 *

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