Engineering a compressed suffix tree implementation

  • Authors:

  • Niko Välimäki;Wolfgang Gerlach;Kashyap Dixit;Veli Mäkinen

  • Affiliations:

  • Department of Computer Science, University of Helsinki, Finland;Technische Fakultät, Universität Bielefeld, Germany;Department of Computer Science and Engineering, Indian Institute of Technology, Kanpur, India;Department of Computer Science, University of Helsinki, Finland

  • Venue:
  • WEA'07 Proceedings of the 6th international conference on Experimental algorithms
  • Year:
  • 2007

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Abstract

Suffix tree is one of the most important data structures in string algorithms and biological sequence analysis. Unfortunately, when it comes to implementing those algorithms and applying them to real genomic sequences, often the main memory size becomes the bottleneck. This is easily explained by the fact that while a DNA sequence of length n from alphabet Σ = {A, C, G, T} can be stored in n log |Σ| = 2n bits, its suffix tree occupies O(n log n) bits. In practice, the size difference easily reaches factor 50. We report on an implementation of the compressed suffix tree very recently proposed by Sadakane (Theory of Computing Systems, in press). The compressed suffix tree occupies space proportional to the text size, i.e. O(n log |Σ|) bits, and supports all typical suffix tree operations with at most log n factor slowdown. Our experiments show that, e.g. on a 10 MB DNA sequence, the compressed suffix tree takes 10% of the space of normal suffix tree. At the same time, a representative algorithm is slowed down by factor 30. Our implementation follows the original proposal in spirit, but some internal parts are tailored towards practical implementation. Our construction algorithm has time requirement O(n log n log |Σ|) and uses closely the same space as the final structure while constructing it: on the 10 MB DNA sequence, the maximum space usage during construction is only 1.4 times the final product size.