Compressed Directed Acyclic Word Graph with Application in Local Alignment

  • Do Huy Hoang
  • Sung Wing Kin
Conference paper

DOI: 10.1007/978-3-642-22685-4_44

Volume 6842 of the book series Lecture Notes in Computer Science (LNCS)
Cite this paper as:
Hoang D.H., Kin S.W. (2011) Compressed Directed Acyclic Word Graph with Application in Local Alignment. In: Fu B., Du DZ. (eds) Computing and Combinatorics. COCOON 2011. Lecture Notes in Computer Science, vol 6842. Springer, Berlin, Heidelberg

Abstract

Suffix tree, suffix array, and directed acyclic word graph (DAWG) are data-structures for indexing a text. Although they enable efficient pattern matching, their data-structures require O(n logn) bits, which make them impractical to index long text like human genome. Recently, the development of compressed data-structures allow us to simulate suffix tree and suffix array using O(n) bits. However, there is still no O(n)-bit data-structure for DAWG with full functionality. This work introduces an O(n)-bit data-structure for simulating DAWG. Besides, we also propose an application of DAWG to improve the time complexity for the local alignment problem. In this application, the previously proposed solutions using BWT (a version of compressed suffix tree) run in O(n2m) worst case time and O(nm0.628) average case time where n and m are the lengths of the database and the query, respectively. Using compressed DAWG proposed in this paper, the problem can be solved in O(nm) worst case time and the same average case time.

Preview

Unable to display preview. Download preview PDF.

Unable to display preview. Download preview PDF.

Copyright information

© Springer-Verlag Berlin Heidelberg 2011

Authors and Affiliations

  • Do Huy Hoang
    • 1
  • Sung Wing Kin
    • 1
  1. 1.National University of Singapore, COM 1Singapore