GPU-Based Cloud Service for Smith-Waterman Algorithm Using Frequency Distance Filtration Scheme

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Provided by: Hindawi Publishing
Topic: Cloud
Format: PDF
As the conventional means of analyzing the similarity between a query sequence and database sequences, the Smith-Waterman algorithm is feasible for a database search owing to its high sensitivity. However, this algorithm is still quite time consuming. CUDA programming can improve computations efficiently by using the computational power of massive computing hardware as Graphics Processing Units (GPUs). This work presents a novel Smith-Waterman algorithm with a frequency-based filtration method on GPUs rather than merely accelerating the comparisons yet expending computational resources to handle such unnecessary comparisons.
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