A fast algorithm on average for all-against-all sequence matching

Author

Baeza-Yates, Ricardo A. ; Gonnet, Gaston H.

Author_Institution

Dept. de Ciencias de la Comput., Chile Univ., Santiago, Chile

fYear

1999

fDate

1999

Firstpage

16

Lastpage

23

Abstract

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

Keywords

biology computing; computational complexity; database theory; dynamic programming; molecular biophysics; string matching; DNA; all-against-all sequence matching; approximate string matching problem; average case analysis; dynamic programming alignment algorithm; fast algorithm; genetic sequences; peptide sequence database; running time; suffix array; Algorithm design and analysis; Computational modeling; DNA; Databases; Dynamic programming; Genetics; Heuristic algorithms; Impedance matching; Peptides; Sequences;

fLanguage

English

Publisher

ieee

Conference_Titel

String Processing and Information Retrieval Symposium, 1999 and International Workshop on Groupware

Conference_Location

Cancun

Print_ISBN

0-7695-0268-7

Type

conf

DOI

10.1109/SPIRE.1999.796573

Filename

796573