Automatic Clustering of DNA Sequences With Intelligent Techniques

Abstract

With the discovery of new DNAs, a fundamental problem arising is how to categorize those DNA sequences into correct species. Unfortunately, identifying all data groups correctly and assigning a set of DNAs into k clusters where k must be predefined are one of the major drawbacks in clustering analysis, especially when the data have many dimensions and the number of clusters is too large and hard to guess. Furthermore, finding a similarity measure that preserves the functionality and represents both the composition and distribution of the bases in a DNA sequence is one of the main challenges in computational biology. In this paper, a new soft computing metaheuristic framework is introduced for automatic clustering to generate the optimal cluster formation and to determine the best estimate for the number of clusters. Pulse coupled neural network (PCNN) is utilized for the calculation of DNA sequence similarity or dissimilarity. Bat algorithm is hybridized with the well-known genetic algorithm to solve the automatic data clustering problem. Extensive computational experiments are conducted on the expanded human oral microbiome database (eHOMD). A comparative study between the experimental results shows that the proposed hybrid algorithm achieved superior performance over the standard genetic algorithm and bat algorithm. Moreover, the hybrid performance was compared with competing algorithms from the literature review to ascertain its superiority. Mann-Whitney-Wilcoxon rank-sum test is conducted to statistically validate the obtained clusters.

Keywords

• DNA sequences
• automatic clustering
• pulse coupled neural network
• genetic algorithm
• bat algorithm