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Protein Structure Prediction (PSP) is the problem of predicting the three-dimensional native structure of a protein given its primary structure, i.e., the corresponding sequence of amino acids. Different approaches have been proposed to model this problem, and this research explores the prediction of optimal structures using the well studied simplified… (More)

a r t i c l e i n f o a b s t r a c t We present a novel technique, suitable for bit-parallelism, for representing both the non-deterministic 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 word of w… (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 best… (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 transloca-tions of equal length adjacent factors and inversions of factors. In… (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)

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(nm max(α, β))-time complexity in the worst case and O(max(α, β))-space… (More)

We investigate the problem of getting to a higher instruction-level 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)

a r t i c l e i n f o a b s t r a c t In this paper we present a method to simulate, using the bit-parallelism technique, the nondeterministic Aho–Corasick automaton and the nondeterministic suffix automaton induced by the trie and by the Directed Acyclic Word Graph for a set of patterns, respectively. When the prefix redundancy is nonnegligible, this… (More)

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)

The Pattern Matching problem with Swaps consists in finding all occurrences of a pattern P in a text T , when disjoint local swaps in the pattern are allowed. In the Approximate Pattern Matching problem with Swaps one seeks to compute, for every text location with a swapped match of P , the number of swaps necessary to obtain a match at the location. In… (More)