2022/11/14 by Martínez-Guardiola, César, Brown, Nathaniel K., Silva-Coira, Fernando +3
#Data Structures and Algorithms (cs.DS) #FOS: Computer and information sciences
paper · doi:10.48550/arxiv.2211.07794
MONI (Rossi et al., 2022) can store a pangenomic dataset T in small space and later, given a pattern P, quickly find the maximal exact matches (MEMs) of P with respect to T. In this paper we consider its one-pass version (Boucher et al., 2021), whose query times are dominated in our experiments by longest common extension (LCE) queries. We show how a small modification lets us avoid most of these queries and thus significantly speeds up MONI in practice while only slightly increasing its size.