English

MONI can find k-MEMs

Data Structures and Algorithms 2022-12-22 v4

Abstract

Suppose we are asked to index a text T[0..n1]T [0..n - 1] such that, given a pattern P[0..m1]P [0..m - 1], we can quickly report the maximal substrings of PP that each occur in TT at least kk times. We first show how we can add O(rlogn)O (r \log n) bits to Rossi et al.'s recent MONI index, where rr is the number of runs in the Burrows-Wheeler Transform of TT, such that it supports such queries in O(kmlogn)O (k m \log n) time. We then show how, if we are given kk at construction time, we can reduce the query time to O(mlogn)O (m \log n).

Keywords

Cite

@article{arxiv.2202.05085,
  title  = {MONI can find k-MEMs},
  author = {Igor Tatarnikov and Ardavan Shahrabi Farahani and Sana Kashgouli and Travis Gagie},
  journal= {arXiv preprint arXiv:2202.05085},
  year   = {2022}
}
R2 v1 2026-06-24T09:30:18.251Z