Emanuele Giaquinta

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The longest common substring with k-mismatches problem is to find, given two strings S1 and S2, a longest substring A1 of S1 and A2 of S2 such that the Hamming distance between A1 and A2 is ≤ k. We introduce a practical O(nm) time and O(1) space solution for this problem, where n and m are the length of S1 and S2, respectively. This algorithm can also be(More)
We present an efficient algorithm for finding all approximate occurrences of a given pattern p of length m in a text t of length n allowing for translocations of equal length adjacent factors and inversions of factors. The algorithm is based on an efficient filtering method and has an O(nmmax(α, β))-time complexity in the worst case and O(max(α, β))space(More)
Given strings P of length m and T of length n over an alphabet of size σ, the string matching with k-mismatches problem is to find the positions of all the substrings in T that are at Hamming distance at most k from P . If T can be read only one character at the time the best known bounds are O(n √ k log k) and O(n+ n √ k/w log k) in the word-RAM model with(More)
Article history: Available online 2 February 2012 We present a novel technique, suitable for bit-parallelism, for representing both the nondeterministic automaton and the nondeterministic suffix automaton of a given string in a more compact way. Our approach is based on a particular factorization of strings which on the average allows to pack in a machine(More)
Given a pattern P and a text T , both strings over a binary alphabet, the binary jumbled string matching problem consists in telling whether any permutation of P occurs in T . The indexed version of this problem, i.e., preprocessing a string to efficiently answer such permutation queries, is hard and has been studied in the last few years. Currently the(More)
We consider how to index strings, trees and graphs for jumbled pattern matching when we are asked to return a match if one exists. For example, we show how, given a tree containing two colours, we can build a quadratic-space index with which we can find a match in time proportional to the size of the match. We also show how we need only linear space if we(More)
The approximate string matching problem consists in finding all locations at which a pattern P of length m matches a substring of a text T of length n, after a given finite number of edit operations. In this paper we investigate such problem when the string distance involves translocations of equal length adjacent factors and inversions of factors. In(More)
We investigate the problem of getting to a higher instructionlevel parallelism in string matching algorithms. In particular, starting from an algorithm based on bit-parallelism, we propose two flexible approaches for boosting it with a higher level of parallelism. These approaches are general enough to be applied to other bit-parallel algorithms. It turns(More)
The exact order-preserving matching problem is to find all the substrings of a text T which have the same length and relative order as a pattern P . Like string maching, order-preserving matching can be generalized by allowing the match to be approximate. In approximate order-preserving matching two strings match if they have the same relative order after(More)