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arXiv · 2202.05085

MONI can find k-MEMs

Igor Tatarnikov·Ardavan Shahrabi Farahani·Sana Kashgouli·Travis Gagie
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Abstract

Suppose we are asked to index a text $T [0..n - 1]$ such that, given a pattern $P [0..m - 1]$, we can quickly report the maximal substrings of $P$ that each occur in $T$ at least $k$ times. We first show how we can add $O (r \log n)$ bits to Rossi et al.'s recent MONI index, where $r$ is the number of runs in the Burrows-Wheeler Transform of $T$, such that it supports such queries in $O (k m \log n)$ time. We then show how, if we are given $k$ at construction time, we can reduce the query time to $O (m \log n)$.

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Igor Tatarnikov, Ardavan Shahrabi Farahani, Sana Kashgouli, Travis Gagie. 2022-02-10. MONI can find k-MEMs. https://arxiv.org/abs/2202.05085

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