Approximate Matching of Run-length Compressed Strings
Veli Mäkinen, Gonzalo Navarro and Esko Ukkonen
We focus on the problem of approximate matching of strings that have been
compressed using run-length encoding. Previous studies have concentrated on the
problem of computing the longest common subsequence (LCS) between two strings
of length m and n compressed to m' and n' runs. We extend
an existing algorithm for the LCS to the Levenshtein distance achieving
O(m'n+n'm) complexity. This approach gives also an algorithm for
approximate searching of a pattern of m letters (m' runs) in a text
of n letters (n' runs) in O(mm'n') time, both for LCS and
Levenshtein models. Then we propose improvements for a greedy algorithm for
the LCS, and conjecture that the improved algorithm has O(m'n') expected
case complexity. Experimental results are provided to support the conjecture.