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Lossless seeds for searching short patterns with high error rates

Abstract

We address the problem of approximate pattern matching using the Levenshtein distance. Given a text T and a pattern P , find all locations in T that differ by at most k errors from P . For that purpose, we propose a filtration algorithm that is based on a novel type of seeds, combining exact parts and parts with a fixed number of errors. Experimental tests show that the method is specifically well-suited for short patterns with a large number of errors
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Dates and versions

hal-01079840 , version 1 (25-11-2019)

Identifiers

  • HAL Id : hal-01079840 , version 1

Cite

Christophe Vroland, Mikaël Salson, Hélène Touzet. Lossless seeds for searching short patterns with high error rates. International Workshop On Combinatorial Algorithms, Oct 2014, Duluth, United States. ⟨hal-01079840⟩
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