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Fast matching statistics in small space
Symposium on Experimental and Efficient Algorithms
Computing the matching statistics of a string S with respect to a string T on an alphabet of size σ is a fundamental primitive for a number of large-scale string analysis applications, including the comparison of entire genomes, for which space is a pressing issue. This paper takes from theory to practice an existing algorithm that uses just O(|T | log σ) bits of space, and that computes a compact encoding of the matching statistics array in O(|S| log σ) time. The techniques used to speed updoi:10.4230/lipics.sea.2018.17 dblp:conf/wea/BelazzouguiCD18 fatcat:bkabknslwbgqtdzpjogw5i3di4