中文

Parse indexing for discarding short pseudo-MEMs safely

数据结构与算法 2026-05-29 v3

摘要

Brown et al.\ (2025) described a pre-processing step, called kk-mer based breaking (KeBaB), that speeds up searching for long maximal exact matches (MEMs) between a pattern PP and an indexed repetitive text TT. KeBaB produces a set of substrings of PP called pseudo-MEMs that often have total length much less than P|P| but are still guaranteed to contain all the MEMs of length at least a fixed parameter kk. Brown et al.\ found that KeBaB can be particularly effective when we discard all but the longest pseudo-MEMs -- but then we risk also discarding the longest MEMs! In this paper we show how we can use parse indexing to generate pseudo-MEMs together with lower bounds on the lengths of the longest MEMs they must contain, allowing us to discard short pseudo-MEMs safely.

引用

@article{arxiv.2605.17574,
  title  = {Parse indexing for discarding short pseudo-MEMs safely},
  author = {Travis Gagie},
  journal= {arXiv preprint arXiv:2605.17574},
  year   = {2026}
}