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Int J Bioinform Res Appl. 2009;5(1):38-49.

A practical algorithm for multiplex PCR primer set selection.

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School of Information Science and Engineering, Central South University, Changsha 410083, China.


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.

[Indexed for MEDLINE]

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