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The Smith-Waterman is one of the most popular algorithms in the molecular sequence alignment. It is often used to find the best local alignment between two strings by calculating the similarity score of the pair of strings. The algorithm is of great potential to be parallelized and has been employed by a lot of FPGA-based solutions, mostly with the systolic array manner. However, the architecture...
Phase change memory (PCM) is a promising technology that can offer higher capacity than DRAM. Unfortunately, PCM's access latency and energy are higher than DRAM's and its endurance is lower. Many DRAM-PCM hybrid memory systems use DRAM as a cache to PCM, to achieve the low access latency and energy, and high endurance of DRAM, while taking advantage of PCM's large capacity. A key question is what...
A flexible hardware architecture that implements a set of new and efficient techniques to significantly reduce the computational requirements of the commonly used Smith–Waterman sequence alignment algorithm is presented. Such innovative techniques use information gathered by the hardware accelerator during the computation of the alignment scores to constrain the size of the subsequence that has to...
Because of the extra ordinary development in electronics technology, flash memories arise as a suitable data storage option for embedded systems. Due to the hardware restrictions and efficiency issues, series of researches has been conducted and are in progress to provide better performance for these devises. One of the popular research areas on flash memories is the state-of-art wear-leveling technique,...
Dynamic programming algorithms are widely used to find the optimal sequence alignment between any two DNA sequences. This paper presents an innovative technique to significantly reduce the computation time and memory space requirements of the traceback phase of the Smith-Waterman algorithm, together with a flexible and scalable hardware architecture to accelerate the overall procedure. The results...
In this paper a BISR architecture for embedded memories is presented. The proposed scheme utilises a multiple bank cache-like memory for repairs. Statistical analysis is used for minimisation of the total resources required to achieve a very high fault coverage. Simulation results show that the proposed BISR scheme is characterised by high efficiency and low area overhead, even for high defect densities...
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