We show how to parallelize the optimal algorithm proposed by Tustumi et al. [19] to solve the all-pairs su x-prefix matching problem for general alphabets. We compared our parallel algorithm with SOF [17], a practical solution for DNA sequences that exhibits good time and space performance in multithreading environments. The experimental results showed that our parallel algorithm achieves a consistent speedup when compared with the sequential algorithm, and it is competitive with SOF when the minimum overlap length is small.
Parallel Computation for the All-Pairs Su x-Prefix Problem
We show how to parallelize the optimal algorithm proposed by Tustumi et al. [19] to solve the all-pairs su x-prefix matching problem for general alphabets. We compared our parallel algorithm with SOF [17], a practical solution for DNA sequences that exhibits good time and space performance in multithreading environments. The experimental results showed that our parallel algorithm achieves a consistent speedup when compared with the sequential algorithm, and it is competitive with SOF when the minimum overlap length is small.