On the k-Hamming and k-Edit Distances

In this paper we consider the weighted k-Hamming and k-Edit distances, that are natural generalizations of the classical Hamming and Edit distances. As main results of this paper we prove that for any k ≥ 2 the DECIS-k-Hamming problem is P-SPACE-complete and the DECIS-k-Edit problem is NEXPTIMEcomplete. In our formulation, weights are included in the instance description and the cost is not uniform

Sequence searching allowing for non-overlapping adjacent unbalanced translocations

Unbalanced translocations are among the most frequent chromosomal alterations, accounted for 30% of all losses of heterozygosity, a major genetic event causing inactivation of tumor suppressor genes. Despite of their central role in genomic sequence analysis, little attention has been devoted to the problem of matching sequences allowing for this kind of chromosomal alteration. In this paper we investigate the approximate string matching problem when the edit operations are non-overlapping unbalanced translocations of adjacent factors. In particular, we first present a O(nm3)-time and O(m2)-space algorithm based on the dynamic-programming approach. Then we improve our first result by designing a second solution which makes use of the Directed Acyclic Word Graph of the pattern. In particular, we show that under the assumptions of equiprobability and independence of characters, our algorithm has a O(n log2σ m) average time complexity, for an alphabet of size σ, still maintaining the O(nm3)-time and the O(m2)-space complexity in the worst case. To the best of our knowledge this is the first solution in literature for the approximate string matching problem allowing for unbalanced translocations of factors

An efficient skip-search approach to swap matching

The swap matching problem consists in finding all occurrences of a pattern x of length m in a text y of length n, allowing for disjoint local swaps of characters in the pattern. In 2003, Amir et al. solved the problem in O(n log m log σ) worst-case time complexity, where σ is the size of the alphabet. In recent years, much research has focused on practical solutions and efficient algorithms have been devised by means of the bit-parallel simulation of non-deterministic automata. In this paper, we present a new efficient algorithm for the swap matching problem based on character comparison and structured as a generalization of the Skip-Search algorithm for the exact string matching problem. Although our solution has a quadratic worst-case time complexity, it shows a sub-linear behaviour on average. According to experimental results, our algorithm obtains in most practical cases the best running times, when compared against the most effective solutions. The gain in speed-up, in terms of running times, is up to 48%. This makes the new algorithm one of the most efficient solutions in practical cases