Dotted Suffix Trees A Structure for Approximate Text Indexing

  • Luís Pedro Coelho
  • Arlindo L. Oliveira
Part of the Lecture Notes in Computer Science book series (LNCS, volume 4209)

Abstract

In this work, the problem we address is text indexing for approximate matching. Given a text \(\mathcal{T}\) which undergoes some preprocessing to generate an index, we can later query this index to identify the places where a string occurs up to a certain number of errors k (edition distance). The indexing structure occupies space \(\mathcal{O}(n\log^kn)\) in the average case, independent of alphabet size. This structure can be used to report the existence of a match with k errors in \(\mathcal{O}(3^k m^{k+1})\) and to report the occurrences in \(\mathcal{O}(3^k m^{k+1} + \mbox{\it ed})\) time, where m is the length of the pattern and ed and the number of matching edit scripts. The construction of the structure has time bound by \(\mathcal{O}(kN|\Sigma|)\), where N is the number of nodes in the index and |Σ| the alphabet size.

Keywords

string algorithms suffix trees approximate text matching text indexing 

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Copyright information

© Springer-Verlag Berlin Heidelberg 2006

Authors and Affiliations

  • Luís Pedro Coelho
    • 1
  • Arlindo L. Oliveira
    • 1
  1. 1.INESC-ID/IST 

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