A Parameterisable and Scalable Smith-Waterman Algorithm Implementation on CUDA-Compatible GPUs

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Provided by: Institute of Electrical & Electronic Engineers
Topic: Hardware
Format: PDF
In this paper, the authors describe a multi-threaded parallel design and implementation of the Smith-Waterman (SM) algorithm on Compute Unified Device Architecture (CUDA)-compatible Graphic Processing Units (GPUs). A novel technique has been put forward to solve the restriction on the length of the query sequence in previous GPU implementations of the Smith-Waterman algorithm. The main reasons behind this limitation in previous GPU implementations were the finite size of local memory and number of threads per block.
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