7914
Lin Ma, Roger D. Chamberlain
Graphics engines are excellent execution platforms for high-throughput computations that exploit a large degree of available parallelism. The achieved performance is, however, highly dependent on the access patterns that the application imposes on the memory subsystem. Here, we propose an analytic model that helps improve the understanding of the performance of memory-limited kernels that employ […]
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Shucai Xiao, Heshan Lin, Wu-chun Feng
The "Basic Local Alignment Search Tool” (BLAST) is arguably the most widely used computational tool in bioinformatics. However, the computational power required for routine BLAST analysis has been outstripping Moore’s Law due to the exponential growth in the size of the genomic sequence databases that BLAST searches on. To address the above issue, we propose […]
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Gang Wei, Chao Ma, Songwen Pei, Baifeng Wu
Sequence alignment is one of the most fundamental and important operation in bioinformatics. Through sequence alignment, we can find the sequence’s information of function, structure and evolution. BLAST is one of the most popular algorithms in the field of sequence alignment. In this paper, we have designed a GPU-based parallel BLAST algorithm and implemented it […]
Huang Lican, Hu Ya
Sequence alignment is one of the most fundamental and important operation in Bioinformatics. Among lots of Sequence alignment tools, Blast is one of the most popular algorithms. In this paper, we describe the primary strategy of a GPU-based parallel computing on Blast program.
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Weiguo Liu, Bertil Schmidt, Wolfgang Muller-Wittig
Scanning protein sequence database is an often repeated task in computational biology and bioinformatics. However, scanning large protein databases, such as GenBank, with popular tools such as BLASTP requires long runtimes on sequential architectures. Due to the continuing rapid growth of sequence databases, there is a high demand to accelerate this task. In this paper, […]
Adrianto Wirawan, Chee Keong K. Kwoh, Nim Tri T. Hieu, Bertil Schmidt
BACKGROUND: The exponential growth of available biological data has caused bioinformatics to be rapidly moving towards a data-intensive, computational science. As a result, the computational power needed by bioinformatics applications is growing exponentially as well. The recent emergence of accelerator technologies has made it possible to achieve an excellent improvement in execution time for many […]
Panagiotis D. Vouzis, Nikolaos V. Sahinidis
MOTIVATION: The Basic Local Alignment Search Tool (BLAST) is one of the most widely used bioinformatics tools. The widespread impact of BLAST is reflected in over 53,000 citations that this software has received in the past two decades, and the use of the word "blast" as a verb referring to biological sequence comparison. Any improvement […]

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