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Time and Space Efficient Search with Suffix Arrays

Yongwook Choi, Jeong Seop Sim, Kun-Soo Park

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Abstract

To search efficiently a text T of length n for a pattern P over an alphabet 5, suffix trees and suffix arrays are widely used. In case of a large text, suffix arrays are preferred to suffix trees because suffix ways take less space than suffix trees. Recently, O(-time and O()-time search algorithms in suffix ways were developed. In this paper we present time and space efficient search algorithms in suffix arrays. One algorithm runs in O() time using O()-bits space, and the other runs in O( time using O(nlog log n/logn)-bits space, which is more space efficient and still fast. Experiments show that our algorithms are efficient in both time and space when compared to previous algorithms.

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What this paper is about

To search efficiently a text T of length n for a pattern P over an alphabet 5, suffix trees and suffix arrays are widely used. In case of a large text, suffix arrays are preferred to suffix trees because suffix ways take less space than suffix trees. Recently, O(-time and O()-time search algorithms in suffix ways were developed. In this paper we present time and space efficient search algorithms in suffix arrays. One algorithm runs in O() time using O()-bits space, and the other runs in O( time using O(nlog log n/logn)-bits space, which is more space efficient and still fast. Experiments show that our algorithms are efficient in both time and space when compared to previous algorithms.

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Available abstract

To search efficiently a text T of length n for a pattern P over an alphabet 5, suffix trees and suffix arrays are widely used. In case of a large text, suffix arrays are preferred to suffix trees because suffix ways take less space than suffix trees. Recently, O(-time and O()-time search algorithms in suffix ways were developed. In this paper we present time and space efficient search algorithms in suffix arrays. One algorithm runs in O() time using O()-bits space, and the other runs in O( time using O(nlog log n/logn)-bits space, which is more space efficient and still fast. Experiments show that our algorithms are efficient in both time and space when compared to previous algorithms.

Key concepts: Suffix, Generalized suffix tree, Compressed suffix array, Suffix tree, Suffix array, Computer science, Space (punctuation), Combinatorics

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