Abstract
We show how to parallelize the optimal algorithm proposed by Tustumi et al. [19] to solve the all-pairs suffix-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.
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Louza, F. A., Gog, S., Zanotto, L., Araujo, G., & Telles, G. P. (2016). Parallel computation for the all-pairs suffix-prefix problem. In Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics) (Vol. 9954 LNCS, pp. 122–132). Springer Verlag. https://doi.org/10.1007/978-3-319-46049-9_12
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