Towards approximate matching in compressed strings: local subsequence recognition

  • Authors:
  • Alexander Tiskin

  • Affiliations:
  • Department of Computer Science, University of Warwick, Coventry, UK

  • Venue:
  • CSR'11 Proceedings of the 6th international conference on Computer science: theory and applications
  • Year:
  • 2011

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Abstract

A grammar-compressed (GC) string is a string generated by a context-free grammar. This compression model includes LZ78 and LZW compression as a special case. We consider the longest common subsequence problem and the local subsequence recognition problem on a GC-text against a plain pattern. We show that, surprisingly, both problems can be solved in time that is within a polylogarithmic factor of the best existing algorithms for the same problems on a plain text. In a wider context presented elsewhere, we use these results as a stepping stone to efficient approximate matching on a GC-text.