Investigating stochastic diffusion search in DNA sequence assembly problem

This paper introduces a novel study on the performance of Stochastic Diffusion Search (SDS) - swarm intelligence algorithm - to address DNA sequence assembly problem. This is an NP-hard problem and one of the primary problems in computational molecular biology that requires optimisation methodologies to reconstruct the original DNA sequence. In this work, SDS algorithm is adapted for the first time for this purpose and several experiments are run in order to evaluate the performance of the presented technique over several frequently used benchmarks. Given the promising results of the newly proposed algorithm and its success in assembling the input fragments, its behaviour is further analysed, thus shedding light on the process through which the algorithm conducts the task. Additionally the performance of the algorithm is compared against several other techniques, demonstrating its weaknesses and strength in the experiments presented in the paper.