Approximate Pattern Matching Over the Burrows-Wheeler Transformed Text
Abstract:
Abstract. The compressed pattern matching problem is to locate the occurrence(s) of a pattern P in a text string T using a compressed representation of T, with minimal (or no) decompression. In this paper, we consider approximate pattern matching directly on Burrow-Wheeler transformed (BWT) text which is a critical step for a fully compressed pattern matching algorithm on a BWT based compression algorithm. The BWT provides a lexicographic ordering of the input text as part of its inverse transformation process. Based on this observation, pattern matching is performed by text pre-filtering, using a fast q-gram intersec-tion of segments from the pattern P and the text T. Algorithms are pro-posed that solve the k-mismatch problem in O(min{m|Σ | k log u u, mu log |Σ | |Σ |}) time worst case, and the k-approximate matching problem in O(|Σ | log |Σ|+ m 2 k u log + αk) time on average (α ≤ u), where u = |T | is the size of
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