A SHARED MEMORY BASED IMPLEMENTATION OF NEEDLEMAN-WUNSCH ALGORITHM USING SKEWING TRANSFORMATION

Vibha Patel, Krunal Gandhi, Darshak Bhatti

Abstract


Among various algorithms for protein and nucleotide alignment, Needleman-Wunsch algorithm is widely accepted as it can divide the problem into sub-problems. We present two parallel approaches of the Needleman-Wunsch algorithm with the single kernel and multi-kernel invocation using skewing transformation which is used for traversing and calculation of dynamic programming matrix. We also compare these with traditional CPU sequential approach which resulted in six-fold performance improvement. Furthermore, we present same single kernel ideology on shared memory which resulted in two-fold performance improvement our non-shared memory approach.

Keywords


Skewing Transformation; CUDA; Single Kernel; Multi-Kernel; Shared Memory; lock-free synchronization

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References


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DOI: https://doi.org/10.26483/ijarcs.v8i9.4953

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