String Processing and Information Retrieval, International Symposium on (1999)
Sept. 21, 1999 to Sept. 24, 1999
Ricardo A. Baeza-Yates , Universidad de Chile
Gaston H. Gonnet , Swiss Federal Institute of Technology
In this paper 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 sub-quadratic with respect to the database size. A similar algorithm solves the approximate string matching problem in sub-linear average time.
R. A. Baeza-Yates and G. H. Gonnet, "A Fast Algorithm on Average for All-Against-All Sequence Matching," String Processing and Information Retrieval, International Symposium on(SPIRE), Cancun, Mexico, 1999, pp. 16.