We develop a novel method of asserting the similarity between two biological sequences without the need for alignment. The proposed method uses free energy of nearest-neighbor interactions as a simple measure of dissimilarity. It is used to perform a search for similarities of a query sequence against three complex datasets. The sensitivity and selectivity are computed and evaluated and the performance of the proposed distance measure is compared. Real data analysis shows that is a very efficient, sensitive and high-selective algorithm in comparing large dataset of DNA sequences.

Key words: Sequence comparison; Nearest-neighbor interaction; Free energy; Sensitivity; Selectivity.

This article can be cited as:
Y. Zhang, W. Chen. A Measure of DNA Sequence Dissimilarity Based on Free Energy of Nearest-neighbor Interaction, J Biomol Struct Dyn 28(4), 557- 565 (2011).