Pattern matching with don't cares and few errors

Authors Raphael Clifford, Klim Efremo, Ely Porat, Amir Rotschild

Thumbnail PDF


  • Filesize: 276 kB
  • 19 pages

Document Identifiers

Author Details

Raphael Clifford
Klim Efremo
Ely Porat
Amir Rotschild

Cite AsGet BibTex

Raphael Clifford, Klim Efremo, Ely Porat, and Amir Rotschild. Pattern matching with don't cares and few errors. In Search Methodologies. Dagstuhl Seminar Proceedings, Volume 9281, pp. 1-19, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2009)


We present solutions for the k-mismatch pattern matching problem with don't cares. Given a text t of length n and a pattern p of length m with don't care symbols and a bound k, our algorithms find all the places that the pattern matches the text with at most k mismatches. We first give an \Theta(n(k + logmlog k) log n) time randomised algorithm which finds the correct answer with high probability. We then present a new deter- ministic \Theta(nk^2 log^m)time solution that uses tools originally developed for group testing. Taking our derandomisation approach further we de- velop an approach based on k-selectors that runs in \Theta(nk polylogm) time. Further, in each case the location of the mismatches at each alignment is also given at no extra cost.
  • Prime Numbers
  • Group Testing
  • Streaming
  • Pattern Matching


  • Access Statistics
  • Total Accesses (updated on a weekly basis)
    PDF Downloads
Questions / Remarks / Feedback

Feedback for Dagstuhl Publishing

Thanks for your feedback!

Feedback submitted

Could not send message

Please try again later or send an E-mail