Computational Biology CB_W0005

Title : AN ANT COLONY SYSTEM FOR DNA SEQUENCE DESIGN BASED ON
THERMODYNAMICS
Author : Tri Basuki Kurniawan1, Noor Khafifah Khalid1, Zuwairie Ibrahim1, Marzuki Khalid1 and Martin Middendorf2
Year : 2008
Place of publish :
Abstract :

 Hybridization between a DNA sequence and its basepairing
complement is crucial to retrieve the information
stored in DNA sequences and operate a computation
operation in DNA computing. Therefore, much works
have focused on designing the DNA sequences to archive
a reliable molecular computation and many algorithms
have been proposed to obtain a set of good DNA
sequences. In this paper, Ant Colony System (ACS) is
proposed to solve the DNA sequence design problem.
ACS as a derivate from Ant Colony Optimization (ACO)
is an improvement from Ant System (AS) that used some
agents to get their solutions based on the pheromone in
their colony. A model is prepared which consists of four
nodes representing four DNA bases using nearestneighbor
thermodynamic parameter’s Watson-Crick base
pair ?Go
37 as the distance between nodes. The results of
the proposed approach are compared with the other
methods such as genetic algorithm and evolutionary
algorithm.