Searching long patterns with BNDM

Jorma Tarhio*

*Corresponding author for this work

Research output: Contribution to journalArticleScientificpeer-review

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Abstract

We present new algorithms for exact string matching of long patterns. Our algorithms read (Formula presented.) -grams at constant distances and are variations of the simplified BNDM algorithm. We demonstrate the competitiveness of our solutions through practical experiments. Many of our algorithms were faster than previous methods for English and DNA patterns between 400 and 50,000 in length. Our algorithms were still better when the preprocessing time was taken into account or when the patterns were taken from a different text of the same type.

Original languageEnglish
Pages (from-to)2160-2169
Number of pages10
JournalSoftware - Practice and Experience
Volume54
Issue number11
Early online date2024
DOIs
Publication statusPublished - Nov 2024
MoE publication typeA1 Journal article-refereed

Keywords

  • exact string matching
  • experimental comparison of algorithms
  • fingerprint
  • q-gram

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