Sequence comparison by exponentially-damped alignment

Abstract

We describe a new method of comparing sequences, based on the Needleman-Wunsch sequence alignment algorithm, which can detect similarities that are interrupted by insertions or deletions in either sequence. The sequences are compared by calculating for each pair of residues a score which represents the best local alignment bringing those residues into correspondence; smooth localisation is achieved by reducing the contribution of distant parts of the alignment path by a factor which decreases exponentially with their distance from the point in question. The calculated values are used to draw a line graph in which regions of local similarity are shown by diagonal lines. Examples are shown of the application of the method to nucleic acid and amino acid sequences.