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This paper introduces a novel method, called Reference-Based String Alignment (RBSA), that speeds up retrieval of optimal subsequence matches in large databases of sequences under the edit distance and the Smith-Waterman similarity measure. RBSA operates using the assumption that the optimal match deviates by a relatively small amount from the query, an amount that does not exceed a prespecified fraction of the query length. RBSA has an exact version that guarantees no false dismissals and can handle large queries efficiently.
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