A new parallel algorithm for computation of statistically significant patterns in DNA sequences

The authors study a method for parallelizing a new algorithm, WORDUP, which detects the presence of statistically significant patterns in DNA sequences. WORDUP implements an efficient method to identify the presence of statistically significant oligomers in a nonhomologous group of sequences. The aim of the parallel version of the WORDUP algorithm is to speed up the computational time and allow the analysis of a greater set of longer nucleotide sequences, which would be impracticable with sequential algorithms. The algorithm has been tested on MEIKO parallel machines, resulting in a substantial improvement in its performance for sequence matching.<
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