A fast algorithm on average for all-against-all sequence matching
Ricardo A. Baeza-Yates, Gastón H. Gonnet · 2003
We present an algorithm which attempts to align pairs of subsequences from a database of genetic sequences. The algorithm simulates the classical dynamic programming alignment algorithm over a suffix array of the database. We provide a detailed average case analysis which shows that the running time of the algorithm is subquadratic with respect to the database size. A similar algorithm solves the approximate string matching problem in sublinear average time.