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

Adding Tightly-Integrated Task Scheduling Acceleration to a RISC-V Multi-core Processor

cces cces

Launching of the Brazilian Initiative on Precision Medicine BIPMed

escience

Bioinformatics applied to biotechnology: A review towards bioenergy research

cces cces