A Similarity Measure for DNA Sequence Analysis Based on Locality

Takashi Yokomori (yokomori@cs.uec.ac.jp)
Satoshi Kobayashi (satoshi@cs.uec.ac.jp)

Department of Computer Science and Information Mathematics
University of Electro-Communications
1-5-1 Chofugaoka, Chofu, Tokyo 182, JAPAN
Tel.: +81-424-83-2161 ex.4375, Fax.: +81-424-82-3055

Abstract

We propose a simple string similarity measure and apply it to the problem of DNA sequence analysis, more specifically, to the problem of analysing molecular evolution. This measure is based on a "local feature" that was motivated from a theoretical characterization on DNA splicing sequences.

We demonstrate the usefulness of the proposed measure by presenting an experimental result which concerns evolutionary molecular analysis. This sheds new light on the other types of DNA sequence analysis such as protein classification, motif identification.