Improving the Mapping of Smith-Waterman Sequence Database Searches onto CUDA-Enabled 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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MOTIVATION Sequence database searching is among the most important and challenging tasks in bioinformatics. The ultimate choice of sequence-search algorithm is that of Smith-Waterman. However, because of the computationally demanding nature of this method, heuristic programs or special-purpose hardware alternatives have been developed. Increased speed has been obtained at the cost of reduced se...
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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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ژورنال
عنوان ژورنال: BioMed Research International
سال: 2015
ISSN: 2314-6133,2314-6141
DOI: 10.1155/2015/185179