Compact Suffix Array — A Space-Efficient Full-Text Index

Issue title: Computing Patterns in Strings

Article type: Research Article

Authors: Mäkinen, Veli

Affiliations: Department of Computer Science, P.O. Box 26 (Teollisuuskatu 23), FIN-00014 University of Helsinki, Finland

Abstract: Suffix array is a widely used full-text index that allows fast searches on the text. It is constructed by sorting all suffixes of the text in the lexicographic order and storing pointers to the suffixes in this order. Binary search is used for fast searches on the suffix array. Compact suffix array is a compressed form of the suffix array that still allows binary searches, but the search times are also dependent on the compression. In this paper, we give efficientmethods for constructing and querying compact suffix arrays. We also study practical issues, such as the trade off between compression and search times, and show how to reduce the space requirement of the construction. Experimental results are provided in comparison with other search methods. With a large text corpora, the index took 1.6 times the size of the text, while the searches were only two times slower than from a suffix array.

Keywords: Suffix array, index compression, full-text index, string matching

Journal: Fundamenta Informaticae, vol. 56, no. 1-2, pp. 191-210, 2003