This paper proposes and evaluates CUDAlign 4.0, a parallel strategy to obtain the optimal
alignment of huge DNA sequences in multi-GPU platforms, using the exact Smith–Waterman …

Several modeling techniques exist to represent agent interaction protocols mostly based on
work done in distributed systems. These modeling techniques do not take the agent features …

This paper proposes and evaluates a parallel strategy to execute the exact Smith-Waterman
(SW) biological sequence comparison algorithm for huge DNA sequences in multi-GPU …

Biological sequence alignment is a very popular application in Bioinformatics, used routinely
worldwide. Many implementations of biological sequence alignment algorithms have been …

Building upon the wide-ranging success of the first edition, Parallel Scientific Computation
presents a single unified approach to using a range of parallel computers, from a small …

Abstract The Smith-Waterman algorithm is used for determining the similarity between two
very long data streams. A popular application of the Smith-Waterman algorithm is for …

Abstract The Smith-Waterman algorithm has a great sensitivity when used for biological
sequence-database searches, but at the expense of high computing-power requirements …

Background We present a performance per watt analysis of CUDAlign 4.0, a parallel
strategy to obtain the optimal pairwise alignment of huge DNA sequences in multi-GPU …

Dynamic programming is an important technique widely used in many scientific applications.
Due to the massive volume of applications' data in practice, parallel and distributed DP is a …

This paper provides a novel hybrid model for solving the multiple pair-wise sequence
alignment problem combining message passing interface and CUDA, the parallel computing …