Title: Using genetic algorithm and maximum clique to design multiplex PCR primers for sequential deletion applications

Authors: Ren-Hao Pan; Rung-Ching Chen; Elong Lin; Yung-Kuan Chan; Yung-Fu Chen

Addresses: Innovation Center for Big Data and Digital Convergence, Yuan Ze University, Chung-Li 32003, Taiwan ' Department of Information Management, Chaoyang University of Technology, Taichung 41349, Taiwan ' Department of Food Science, Central Taiwan University of Science and Technology, Taichung 40601, Taiwan ' Department of Management Information System, National Chung Hsing University, Taichung 40227, Taiwan ' Department of Dental Technology and Materials Science, Central Taiwan University of Science and Technology, Taichung 40601, Taiwan; Department of Health Services Administration, China Medical University, Taichung 40402, Taiwan

Abstract: Sequential deletion method is generally used to locate the functional domain of a protein. In contrast to the general Multiplex Polymerase Chain Reaction (MPCR) that requires multiple pairs of forward and reverse primers to extract the desired products, the MPCR for sequential deletion also needs multiple forward primers, which are clustered into several groups, but only a single compatible reverse primer in each corresponding group. In this study, a Genetic-Maximum-Clique (GMC) algorithm which combines the genetic algorithm for solving maximum clique problem is proposed to design the primers of MPCR. This algorithm obtains near-optimal primers that can be clustered in as few multiplex primer groups as possible for one PCR experiment. The results show that the algorithm can provide fewer groups for longer sequences. It is useful in assisting the researchers to design the primers for multiplex PCR experiments specific to sequential deletion applications. Furthermore, primers designed by the proposed GMC method has also been confirmed to be capable of covering the primers designed manually in previous investigations.

Keywords: multiplex PCR; polymerase chain reaction; sequential deletion applications; truncated mutant; genetic algorithms; maximum clique; PCR primer design; web services; bioinformatics.

DOI: 10.1504/IJDMB.2016.074686

International Journal of Data Mining and Bioinformatics, 2016 Vol.14 No.2, pp.177 - 195

Received: 11 Sep 2014
Accepted: 15 May 2015
Published online: 13 Feb 2016 *

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