Optimal Spaced Seeds for Faster Approximate String Matching

Filtering is a standard technique for fast approximate string matching in practice. In filtering, a quick first step is used to rule out almost all positions of a text as possible starting positions for a pattern. Typically this step consists of finding the exact matches of small parts of the pattern. In the followup step, a slow method is used to verify or eliminate each remaining position. The running time of such a method depends largely on the quality of the filtering step, as measured by its false positives rate. The quality of such a method depends on the number of true matches that it misses, that is, on its false negative rate. A spaced seed is a recently introduced type of filter pattern that allows gaps (i.e. don’t cares) in the small sub-pattern to be searched for. Spaced seeds promise to yield a much lower false positives rate, and thus have been extensively studied, though heretofore only heuristically or statistically. In this paper, we show how to design almost o...

• Type: Conference
• Year: 2005
• Where: ICALP
• Authors: Martin Farach-Colton, Gad M. Landau, Süleyman Cenk Sahinalp, Dekel Tsur
• Keywords: False Negatives, False Positives Rate, ICALP 2005, Spaced Seeds, Theoretical Computer Science