TY - JOUR

T1 - Faster algorithms for string matching with k mismatches

AU - Amir, Amihood

AU - Lewenstein, Moshe

AU - Porat, Ely

PY - 2000/1/1

Y1 - 2000/1/1

N2 - The string matching with mismatches problem is that of finding the number of mismatches between pattern P of length m and every length m substring of the text T. Currently, the best algorithms for this problem are the following. The Landau-Vishkin algorithm finds all locations where the pattern has at most k errors (where k is part of the input) in time O(nk). The Abrahamson algorithm finds the number of mismatches at every location in time O(n√m log m). We present an algorithm that is faster than both. Our algorithm finds all locations where the pattern has at most k errors in time O(n√k log k). We also show an algorithm that solves the above problem in time O((n+nk3/m) log k).

AB - The string matching with mismatches problem is that of finding the number of mismatches between pattern P of length m and every length m substring of the text T. Currently, the best algorithms for this problem are the following. The Landau-Vishkin algorithm finds all locations where the pattern has at most k errors (where k is part of the input) in time O(nk). The Abrahamson algorithm finds the number of mismatches at every location in time O(n√m log m). We present an algorithm that is faster than both. Our algorithm finds all locations where the pattern has at most k errors in time O(n√k log k). We also show an algorithm that solves the above problem in time O((n+nk3/m) log k).

UR - http://www.scopus.com/inward/record.url?scp=33903571&partnerID=8YFLogxK

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JO - Proceedings of the Annual ACM-SIAM Symposium on Discrete Algorithms

JF - Proceedings of the Annual ACM-SIAM Symposium on Discrete Algorithms

ER -