https://hal.archives-ouvertes.fr/hal-00741966Crochemore, MaximeMaximeCrochemoreInformatics - King‘s College LondonLIGM - Laboratoire d'Informatique Gaspard-Monge - UPEM - Université Paris-Est Marne-la-Vallée - ENPC - École des Ponts ParisTech - ESIEE Paris - Fédération de Recherche Bézout - CNRS - Centre National de la Recherche ScientifiqueS. Iliopoulos, CostasCostasS. IliopoulosInformatics - King‘s College LondonP. Pissis, SolonSolonP. PissisInformatics - King‘s College LondonA Parallel Algorithm for Fixed-Length Approximate String-Matching with k-mismatchesHAL CCSD2010[INFO.INFO-DS] Computer Science [cs]/Data Structures and Algorithms [cs.DS]Crochemore, MaximeTapio Elomaa, Heikki Mannila, Pekka Orponen2013-02-13 11:24:012022-09-29 14:21:152013-02-13 14:20:56enBook sectionsapplication/pdf1This paper deals with the approximate string-matching problem with Hamming distance. The approximate string-matching with kmismatches problem is to ﬁnd all locations at which a query of length m matches a factor of a text of length n with k or fewer mismatches. The approximate string-matching algorithms have both pleasing theoretical features, as well as direct applications, especially in computational biology. We consider a generalisation of this problem, the ﬁxed-length approximate string-matching with k-mismatches problem: given a text t, a pattern x and an integer l, search for all the occurrences in t of all factors of x of length l with k or fewer mismatches with a factor of t. We present a practical parallel algorithm of comparable simplicity that requires only O(nm(l/w)/p) time, where w is the word size of the machine (e.g. 32 or 64 in practice) and p the number of processors. Thus the algorithm's performance is independent of k and the alphabet size |Σ|. The proposed parallel algorithm makes use of message-passing parallelism model, and word-level parallelism for efficient approximate string-matching.