Accelerating Smith-Waterman Algorithm for Biological Database Search on CUDA-Compatible GPUs
نویسندگان
چکیده
منابع مشابه
Improving the Mapping of Smith-Waterman Sequence Database Searches onto CUDA-Enabled GPUs
Sequence alignment lies at heart of the bioinformatics. The Smith-Waterman algorithm is one of the key sequence search algorithms and has gained popularity due to improved implementations and rapidly increasing compute power. Recently, the Smith-Waterman algorithm has been successfully mapped onto the emerging general-purpose graphics processing units (GPUs). In this paper, we focused on how to...
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Given two strings S1 = pqaxabcstrqrtp and S2 = xyaxbacsl, the substrings axabcs in S1 and axbacs in S2 are very similar. The problem of finding similar substrings is the local alignment problem. Local alignment is extensively used in computational biology to find regions of similarity in different biological sequences. Similar genetic sequences are identified by computing the local alignment of...
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The Smith-Waterman (SW) algorithm has been widely utilized for searching biological sequence databases in bioinformatics. Recently, several works have adopted the graphic card with Graphic Processing Units (GPUs) and their associated CUDA model to enhance the performance of SW computations. However, these works mainly focused on the protein database search by using the intertask parallelization...
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ژورنال
عنوان ژورنال: IEICE Transactions on Information and Systems
سال: 2010
ISSN: 0916-8532,1745-1361
DOI: 10.1587/transinf.e93.d.1479