Approximate String Matching over Ziv-Lempel Compressed Text

Abstract. We present a solution to the problem of performing approximate pattern matching on compressed text. The format we choose is the Ziv-Lempel family, speci cally the LZ78 and LZW variants. Given a text of length u compressed into length n, and a pattern of length m, we report all the R occurrences of the pattern in the text allowing up to k insertions, deletions and substitutions, in O(mkn+R) time. The existence problem needs O(mkn) time. We also show that the algorithm can be adapted to run in O(k2 n + min(mkn;m2 (m )k ) + R) average time, where is the alphabet size. The experimental results show a speedup over the basic approach for moderate m and small k.

• Type: Conference
• Year: 2000
• Where: CPM
• Authors: Juha Kärkkäinen, Gonzalo Navarro, Esko Ukkonen
• Keywords: Combinatorics, CPM 2000, Length M, Pattern Matching, Ziv-Lempel Family