Affiliation:
1. Universität Karlsruhe, Karlsruhe, Germany
2. University of Helsinki, Finland
3. Max-Planck-Institut für Informatik, Saarbrücken, Germany
Abstract
Suffix arrays are a simple and powerful data structure for text processing that can be used for full text indexes, data compression, and many other applications, in particular, in bioinformatics. However, so far, it has appeared prohibitive to build suffix arrays for huge inputs that do not fit into main memory. This paper presents design, analysis, implementation, and experimental evaluation of several new and improved algorithms for suffix array construction. The algorithms are asymptotically optimal in the worst case or on average. Our implementation can construct suffix arrays for inputs of up to 4-GB in hours on a low-cost machine. As a tool of possible independent interest, we present a systematic way to design, analyze, and implement
pipelined
algorithms.
Publisher
Association for Computing Machinery (ACM)
Subject
Theoretical Computer Science
Cited by
36 articles.
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