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Large-scale protein sequence comparison is an important but compute-intensive task in molecular biology. BLASTP is the most popular tool for comparative analysis of protein sequences. In recent years, an exponential increase in the size of protein sequence databases has required either exponentially more running time or a cluster of machines to keep pace.(More)
Comparison between biosequences and probabilistic models is an increasingly important part of modern DNA and protein sequence analysis. The large and growing number of such models in today's databases demands computational approaches to searching these databases faster, while maintaining high sensitivity to biologically meaningful similarities. This work 1(More)
GPUs devices are becoming critical building blocks of High-Performance platforms for performance and energy efficiency reasons. As a consequence, parallel programming environment such as OpenMP were extended to support offloading code to such devices. OpenMP compilers are faced with offering an efficient implementation of device-targeting constructs. One(More)
BLASTP is the most popular tool for comparative analysis of protein sequences. In recent years, an exponential increase in the size of protein sequence databases has required either exponentially more runtime or a cluster of machines to keep pace. To address this problem, we have designed and built a high-performance FPGA-accelerated version of BLASTP,(More)
A s the amount of scientific and social data continues to grow, researchers in a multitude of domains face challenges associated with storing, indexing, retrieving, assimilating, and synthesizing raw data into actionable information. Combining techniques from computer science , statistics, and applied math, data-intensive computing involves developing and(More)
Many studies point to the difficulty of scaling existing computer architectures to meet the needs of an exascale system (i.e., capable of executing 10 18 floating-point operations per second), consuming no more than 20 MW in power, by around the year 2020. This paper outlines a new architecture, the Active Memory Cube, which reduces the energy of(More)
RNA structure prediction, or folding, is a compute-intensive task that lies at the core of several search applications in bioinformatics. We begin to address the need for high-throughput RNA folding by accelerating the Nussi-nov folding algorithm using a 2D systolic array architecture. We adapt classic results on parallel string parenthe-sization to produce(More)
Large-scale protein sequence comparison is an important but compute-intensive task in molecular biology. The popular BLASTP software for this task has become a bottleneck for proteomic database search. One third of this software's time is spent executing the Smith-Waterman dynamic programming algorithm. This work describes a novel FPGA design for banded(More)
—RNA folding is a compute-intensive task that lies at the core of search applications in bioinformatics such as RNAfold and UNAFold. In this work, we analyze the Zuker RNA folding algorithm, which is challenging to accelerate because it is resource intensive and has a large number of variable-length dependencies. We use a technique of Lyngsø to rewrite the(More)
N-Gram (n-character sequences in text documents) counting is a well-established technique used in classifying the language of text in a document. In this paper, n-gram processing is accelerated through the use of reconfigurable hardware on the XtremeData XD1000 system. Our design employs parallelism at multiple levels, with parallel Bloom Filters accessing(More)