Tuning BNDM with q-grams

DOI10.1137/1.9781611972894.3MaRDI QIDQ5233563zbMATH OpenOpenAlexFDO

Authors Branislav Ďurian, Jan Holub, Hannu Peltola, Jorma Tarhio

Publication date 11 September 2019

Published in 2009 Proceedings of the Eleventh Workshop on Algorithm Engineering and Experiments (ALENEX) (Search for Journal in Brave)

Full work available at URL https://doi.org/10.1137/1.9781611972894.3

Mathematics Subject Classification ID

Natural language processing (68T50) Parallel algorithms in computer science (68W10) Algorithms on strings (68W32) Protein sequences, DNA sequences (92D20)

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(6)

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• Byte-aligned pattern matching in encoded genomic sequences
• Faster string matching based on hashing and bit-parallelism
• Alternative algorithms for bit-parallel string matching.
• Improving practical exact string matching

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