Space efficient linear time construction of suffix arrays

  • Authors:

  • Pang Ko;Srinivas Aluru

  • Affiliations:

  • Laurence H. Baker Center for Bioinformatics and Biological Statistics, Iowa State University, Ames, IA;Dept. of Electrical and Computer Engineering and Laurence H. Baker Center for Bioinformatics and Biological Statistics, Iowa State University, Ames, IA

  • Venue:
  • CPM'03 Proceedings of the 14th annual conference on Combinatorial pattern matching
  • Year:
  • 2003

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Abstract

We present a linear time algorithm to sort all the suffixes of a string over a large alphabet of integers. The sorted order of suffixes of a string is also called suffix array, a data structure introduced by Manber and Myers that has numerous applications in pattern matching, string processing, and computational biology. Though the suffix tree of a string can be constructed in linear time and the sorted order of suffixes derived from it, a direct algorithm for suffix sorting is of great interest due to the space requirements of suffix trees. Our result improves upon the best known direct algorithm for suffix sorting, which takes O(n log n) time. We also show how to construct suffix trees in linear time from our suffix sorting result. Apart from being simple and applicable for alphabets not necessarily of fixed size, this method of constructing suffix trees is more space efficient.