A practical algorithm for multiplex PCR primer set selection

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.

[1]  Richard Schoske,et al.  Multiplex PCR design strategy used for the simultaneous amplification of 10 Y chromosome short tandem repeat (STR) loci , 2003, Analytical and bioanalytical chemistry.

[2]  Pierre Nicodeme.  A Computer Support for Genotyping by Multiplex PCR , 1995 .

[3]  Jorng-Tzong Horng,et al.  Primer design for multiplex PCR using a genetic algorithm , 2003, GECCO '05.

[4]  Alexander Russell,et al.  Minimum Multicolored Subgraph Problem in Multiplex PCR Primer Set Selection and Population Haplotyping , 2006, International Conference on Computational Science.

[5]  Cheng-Yan Kao,et al.  Designing Multiple-Use Primer Set for Multiplex PCR by Using Compact GAs , 2004, PPSN.

[6]  Kishori M. Konwar,et al.  Approximation Algorithms for Minimum PCR Primer Set Selection with Amplification Length and Uniqueness Constraints , 2004, ArXiv.

[7]  Doi,et al.  Greedy Algorithms for Finding a Small Set of Primers Satisfying Cover and Length Resolution Conditions in PCR Experiments. , 1997, Genome informatics. Workshop on Genome Informatics.

[8]  Jean-Marc Steyaert,et al.  Selecting Optimal Oligonucleotide Primers for Multiplex PCR , 1997, ISMB.

[9]  William R. Pearson,et al.  On the Primer Selection Problem in Polymerase Chain Reaction Experiments , 1996, Discret. Appl. Math..

[10]  Li Maojun,et al.  A PARTHENO GENETIC ALGORITHM AND ANALYSIS ON ITS GLOBAL CONVERGENCE , 1999 .

[11]  Steven Skiena,et al.  Microarray synthesis through multiple-use PCR primer design , 2002, ISMB.

[12]  Thomas Kämpke,et al.  Efficient primer design algorithms , 2001, Bioinform..

[13]  Doi,et al.  A Greedy Algorithm for Minimizing the Number of Primers in Multiple PCR Experiments. , 1999, Genome informatics. Workshop on Genome Informatics.

[14]  Kishori M. Konwar,et al.  Improved algorithms for multiplex PCR primer set selection with amplification length constraints , 2005, APBC.

[15]  Jain-Shing Wu,et al.  Multiplex PCR primer design for gene family using genetic algorithm , 2005, GECCO '05.