SIMD parallelization of the WORDUP algorithm for detecting statistically significant patterns in DNA sequences

The development of new techniques in sequencing nucleic acidshas produced a great amount of sequence data and has led tothe discovery of new relationships. In this paper, we studya method for parallelizing the algorithm WORDUP, which detectsthe presence of statistically significant patterns in DNA sequences.WORDUP implements an efficient method to identify the presenceof statistically significant oligomers in a nonhomologous groupof sequences. It is based on a modified version of the Boyer-Moorealgorithm, which is one of the fastest algorithms for stringmatching available in the literature. The aim of the parallelversion of WORDUP presented here is to speed up the computationaltime and allow the analysis of a greater set of longer nucleotidesequences, which is usually impractical with sequential algorithms.