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Communication Dans Un Congrès Année : 2019

Streaming k-mismatch with error correcting and applications

Résumé

We present a new streaming algorithm for the k-Mismatch problem, one of the most basic problems in pattern matching. Given a pattern and a text, the task is to find all substrings of the text that are at the Hamming distance at most k from the pattern. Our algorithm is enhanced with an important new feature called Error Correcting, and its complexities for k = 1 and for a general k are comparable to those of the solutions for the k-Mismatch problem by Porat and Porat (FOCS 2009) and Clifford et al. (SODA 2016). In parallel to our research, a yet more efficient algorithm for the k-Mismatch problem with the Error Correcting feature was developed by Clifford et al. (SODA 2019). Using the new feature and recent work on streaming Multiple Pattern Matching we develop a series of streaming algorithms for pattern matching on weighted strings, which are a commonly used representation of uncertain sequences in molecular biology. We also show that these algorithms are space-optimal up to polylog factors. A preliminary version of this work was published at DCC 2017 conference [24].
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Dates et versions

hal-03942923 , version 1 (17-01-2023)

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  • HAL Id : hal-03942923 , version 1

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Jakub Radoszewski, Tatiana Starikovskaya. Streaming k-mismatch with error correcting and applications. Conference Data Compression Conference (DCC) 2017, 2017, Snowbird (USA), United States. ⟨hal-03942923⟩
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