Rodolfo Bezerra Batista

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Pairwise Sequence Alignment is a basic operation in Bioinformatics that is performed thousands of times, in a daily basis. The exact methods proposed in the literature have quadratic time complexity. For this reason, heuristic methods such as BLAST are widely used. Nevertheless, it is known that exact methods present better sensitivity, leading to better(More)
Summary form only given. Biological inspired techniques have proven to be efficient in solving a variety of real problems using parallel and distributed processing. In this paper, we wish to study the DNA sequencing problem known for its computational requirements which far exceed the computing capabilities of the fastest available sequential machines.(More)
Sequence comparison is a basic operation in DNA sequencing projects, and most sequence comparison methods used are based on heuristics, that are faster but do not produce optimal alignments. Recently, many organisms have had their DNA entirely sequenced, and this reality presents the need for comparing long DNA sequences, which is a challenging task due to(More)
Distributed Shared Memory systems allow the use of the shared memory programming paradigm in distributed architectures where no physically shared memory exist. Scope consistent software DSMs provide a relaxed memory model that reduces the coherence overhead by ensuring consistency only at synchronization operations, on a per-lock basis. Much of the work in(More)
The algorithm proposed by Smith-Waterman is an exact method that obtains optimal local alignments in quadratic space and time. For long sequences, quadratic complexity makes the use of this algorithm impractical. In this scenario, parallel computing is a very attractive alternative. In this paper, we propose and evaluate z-align, a parallel exact strategy(More)
Sequence Alignment is a basic operation in Bioinformatics that is performed thousands of times, on daily basis. The exact methods for pairwise alignment have quadratic time complexity. For this reason, heuristic methods such as BLAST are widely used. To obtain exact results faster, parallel strategies have been proposed but most of them fail to align huge(More)
Distributed shared memory systems allow the use of the shared memory programming paradigm in distributed architectures where no physically shared memory exist. To reduce coherence overhead, relaxed memory consistency models were proposed. Scope consistent software DSMs provide a relaxed memory model that guarantees consistency only at synchronization(More)
The algorithm proposed by Smith-Waterman is an exact method that obtains optimal local alignments in quadratic space and time. For long sequences, quadratic complexity makes the use of this algorithm impractical. In this scenario, parallel computing is a very attractive alternative. In this paper, we propose and evaluate z-align, a parallel exact strategy(More)