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GPU Computing Gems Emerald Edition by Wen-mei W. Hwu

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Chapter 11. Accurate Scanning of Sequence Databases with the Smith-Waterman Algorithm
Łukasz Ligowski, Witold R. Rudnicki, Yongchao Liu and Bertil Schmidt
Because of the advances in high-throughput sequencing technologies, publicly available protein sequence databases continue to grow rapidly. Biologists frequently need to scan these databases to find similar sequences in order to annotate a query sequence of unknown functionality. In this chapter we present how the dynamic programming-based Smith-Waterman (SW) algorithm for protein sequence database scanning can be optimized on GPUs. Starting from a basic CUDA implementation, we discuss several optimization techniques using shared memory, registers, loop unrolling, and CPU/GPU partitioning. ...

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