The prefix table of a string is one of the most fundamental data structures of algorithms on strings: it determines the longest factor at each position of the string that matches a prefix of the string. It can be computed in time linear with respect to the size of the string, and hence it can be used efficiently for locating patterns or for regularity searching in strings. A weighted string is ...

If DNA were a random string over its alphabet fA;C;G; Tg, an optimal code would assign 2 bits to each nucleotide. DNA may be imagined to be a highly ordered, purposeful molecule, and one might therefore reasonably expect statistical models of its string representation to produce much lower entropy estimates. Surprisingly this has not been the case for many natural DNA sequences, including porti...

The k differences approximate string matching problem specifies a text string of length n, a pattern string of length m, the number k of differences (insertions, deletions, substitutions) allowed in a match, and asks for every location in the text where a match occurs. Previous algorithms require at least O(nk) time. When k is as large as a fraction of m, no substantial progress has been made o...

If DNA were a random string over its alphabet {A, C, G, T}, an optimal code would assign two bits to each nucleotide. DNA may be imagined to be a highly ordered, purposeful molecule, and one might therefore reasonably expect statistical models of its string representation to produce much lower entropy estimates. Surprisingly, this has not been the case for many natural DNA sequences, including ...

In this paper we describe teoretical solution and practical usage of a Finite State Automata (FSA) in one and n-dimensional space. We classify approximate pattern matching problems using algebraic structures. Construction of algebra for pattern matching and operations applied to FSA corresponds to the creation of new pattern matching problems. We present several operations and describe some ide...

The electrostatic complexes of polyanionic DNA with cationic dendrimer have been considered as a potential non-viral vector for gene delivery and a model system for understanding DNA-histone interaction. Although it is believed that the gene transfection efficiency may be influenced by the structure of the complex, the supramolecular structure of DNA-dendirmer complexes and its dependence on va...

In this paper, we study methods for improving the efficiency and privacy of compressed DNA sequence comparison computations, under various querying scenarios. For instance, one scenario involves a querier, Bob, who wants to test if his DNA string, Q, is close to a DNA string, Y , owned by a data owner, Alice, but Bob does not want to reveal Q to Alice and Alice is willing to reveal Y to Bob onl...