Optimization schemes and performance evaluation of Smith-Waterman algorithm on CPU, GPU and FPGA.

Dan Zhou Yong Dou Fei Xia

Published in: Concurr. Comput. Pract. Exp. (2012)

Keyphrases

k means
parallel implementation
similarity measure
dynamic programming
hardware implementation
optimal solution
roc curve
gpu implementation
objective function
data structure
np hard
lower and upper bounds
sequence alignment
graphics processors