CCES Unicamp

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.
Parallel Computation for the All-Pairs Su x-Prefix Problem

Full Article URL:

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.

Related posts

Theoretical insights about the possibility of removing Pb2+ and Hg2+ metal ions using adsorptive processes and matrices of carboxymethyl diethylaminoethyl cellulose and cellulose nitrate biopolymers

cces cces

III CCES Workshop & SAIMS

escience

Parallel programming education at the CCES

cces cces