Function Minimization In DNA Sequence Design Based On Binary Particle Swarm Optimization

TL;DR: In this paper, a binary particle swarm optimization (BinPSO) is proposed to minimize the objective functions individually, subjected to two constraints: melting temperature and GCcontent. And the results obtained show the correctness of PSO computation, where the minimized values for each objective can be achieved.

Abstract: In DNA based computation and DNA nanotechnology, the design of good DNA sequences has turned out to be an elementary problem and one of the most practical and important research topics. Although the design of DNA sequences is dependent on the protocol of biological experiments, it is highly required to establish a method for the systematic design of DNA sequences, which could be applied to various design constraints. Basically, the fitness of DNA sequences can be evaluated using four objective functions, namely, similarity, Hmeasure, continuity and hairpin. In this paper, binary particle swarm optimization (BinPSO) is proposed to minimize those objective functions individually, subjected to two constraints: melting temperature and GCcontent. An implementation of the optimization process is presented using 20 particles and the results obtained shows the correctness of PSO computation, where the minimized values for each objective can be achieved. Kata kunci: DNA sequence design; binary particle swarm optimization; objective function; constraints; fitness function Dalam DNA berasaskan pengiraan dan nanoteknologi DNA, reka bentuk jujukan–jujukan DNA baik telah menjadi satu masalah asas dan salah satu topik–topik penyelidikan penting dan paling praktikal. Walaupun reka bentuk DNA berjujukan adalah bergantung kepada pada protokol eksperimen biologi, ia amat diperlukan bagi mewujudkan satu kaedah untuk reka bentuk bersistem DNA berjujukan, yang boleh digunakan untuk pelbagai reka bentuk kekangan. Pada asasnya, kecergasan DNA berjujukan boleh dinilaikan menggunakan empat fungsi–fungsi objektif, iaitu, similarity, Hmeasure, continuity dan hairpin. Dalam kertas kerja ini, pengoptimuman kerumunan zarah perduaan (BinPSO) dicadangkan untuk meminimumkan fungsi–fungsi objektif tersebut secara individu, tertakluk kepada dua kekangan: melting temperature dan GCcontent Satu perlaksanaan proses pengoptimuman dibentangkan menggunakan 20 zarah–zarah dan keputusan yang diperolehi menunjukkan kebenaran pengiraan PSO, di mana nilai–nilai yang minimum untuk setiap objektif dapat dicapai. Key words: Reka bentuk jujukan DNA; pengoptimuman kerumunan zarah perduaan; fungsi objektif; kekangan; fungsi kecergasan