A Method of Genome Sequence Comparison Based on a New Form of Fuzzy Polynucleotide Space

Abstract

Genome sequence similarity targeted to actual biological taxa is one of the foremost challenging tasks. Several attempts are taken to represent whole-genome sequences using standard fuzzy polynucleotide metric spaces. Nevertheless, in this space, intuitively similar sequences are found to be dissimilar under the NTV metric and all the metrics do not behave similarly in all genome sequences. In this paper, a new form of sixteen-dimensional fuzzy polynucleotide space is proposed over a unit hypercube. Furthermore, to measure similarity/dissimilarity between these fuzzy polynucleotides a modified form of the standard NTV metric is introduced. The method is verified on whole-genome sequences of Corynebacterium diphtheriae, Haemophilus influenza, Halobacterium sp. and Xylella fastidiosa. The proposed technique produces consistent and satisfactory results in all such cases. The results indicate that this new form of fuzzy polynucleotide space with the modified form of NTV metric is satisfactory for genome sequence comparison.