Linear-time construction of compressed suffix arrays using o(n log n)-bit working space for large alphabets

Abstract

The suffix array is a fundamental index data structure in string algorithms and bioinformatics, and the compressed suffix array (CSA) and the FM-index are its compressed versions. Many algorithms for constructing these index data structures have been developed. Recently, Hon et al. [11] proposed a construction algorithm using O(n · log log |∑|) time and O(n log |∑|)-bit working space, which is the fastest algorithm using O(n log |∑|)-bit working space. In this paper we give an efficient algorithm to construct the index data structures for large alphabets. Our algorithm constructs the suffix array, the CSA, and the FM-index using O(n) time and O(n log |∑| log |∑|α n)-bit working space, where α = log3 2. Our algorithm takes less time and more space than Hon et al.'s algorithm. Our algorithm uses least working space among alphabet-independent linear-time algorithms. © Springer-Verlag Berlin Heidelberg 2005.