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A Study of the Contribution of Nearest-Neighbour Thermodynamic Parameters to the DNA Sequences Generated by Ant Colony Optimisation

Mohd Zaidi, Mohd Tumari and Zuwairie, Ibrahim and Kamarul Hawari, Ghazali and Faradila, Naim and Mohd Falfazli, Mat Jusof and Ismail, Ibrahim and Zulkifli, Md. Yusof and Kamal, Khalil and Muhammad Arif, Abdul Rahim and Sophan Wahyudi, Nawawi (2013) A Study of the Contribution of Nearest-Neighbour Thermodynamic Parameters to the DNA Sequences Generated by Ant Colony Optimisation. In: International Conference of Modelling Identification and Control (ICMIC2013), 31 August - 2 September 2013 , Cairo, Egypt. pp. 287-291..

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Abstract

The process of designing a set of good DNA sequences is an essential problem and one of the most practical and important research topics in DNA-based computing and the DNA nanotechnology area. In this field of research, a DNA sequence design problem is defined as a multi-objective problem, and it is evaluated using four objective functions, h-measure, similarity, continuity and hairpin. In addition, two constraints, GC content and melting temperature (Tm), are used to maintain uniform chemical characteristics of the sequences. In the authors’ previous research, an ant colony system (ACS) was proposed to solve the DNA sequence design problem based on nearest neighbour. The Watson-Crick base pair ∆Go37 was used as the distance between nodes for the thermodynamic parameters in the problem models for the heuristic approach in the ACS algorithms. In the current study, a non-heuristic approach and four new models using the heuristic approach are proposed, and results from the models are compared.

Item Type: Conference or Workshop Item (Speech)
Uncontrolled Keywords: Ant colony optimization; DNA sequence design; Nearest-neighbour thermodynamic
Subjects: T Technology > TK Electrical engineering. Electronics Nuclear engineering
Faculty/Division: Faculty of Electrical & Electronic Engineering
Depositing User: Noorul Farina Arifin
Date Deposited: 06 May 2014 07:36
Last Modified: 21 Feb 2018 01:57
URI: http://umpir.ump.edu.my/id/eprint/5675
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