A New Algorithm for Fast All-Against-All Substring Matching
- Cite this paper as:
- Barsky M., Stege U., Thomo A., Upton C. (2006) A New Algorithm for Fast All-Against-All Substring Matching. In: Crestani F., Ferragina P., Sanderson M. (eds) String Processing and Information Retrieval. SPIRE 2006. Lecture Notes in Computer Science, vol 4209. Springer, Berlin, Heidelberg
We present a new and efficient algorithm to solve the ’threshold all vs. all’ problem, which involves searching of two strings (with length N and M respectively) for finding all maximal approximate matches of length at least S and with up to K differences. The algorithm is based on a novel graph model, and it solves the problem in time O(NMK2).
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