The development of new twchniques in sequencing nucleid acids has producted a great amount of sequence data and has led to the discovery of new relationships. In this paper we study a method for parallelizing the algorithm WORDUP, which detects the presence of statistically significant patterns in DNA squences. WORDUP implemnets an efficient method to identify the presence of statistically significant oligomers in a non-homolous group of sequences. Is is based on a modified version of the Boyer-Moor algorithm, which is one of the fastest algorithms for string mathcing available in the literature. The aim of the parallel version of WORDUP presented here is to speed up the computational time and allow the analysis of a greater set of longer nucleotide sequences, which is usually impratical with sequential algorithms.
SIMD parallelization of WORDUP algorithm for detection statistically significant patterns in DNA sequences
T D'Orazio;E Stella;
1993
Abstract
The development of new twchniques in sequencing nucleid acids has producted a great amount of sequence data and has led to the discovery of new relationships. In this paper we study a method for parallelizing the algorithm WORDUP, which detects the presence of statistically significant patterns in DNA squences. WORDUP implemnets an efficient method to identify the presence of statistically significant oligomers in a non-homolous group of sequences. Is is based on a modified version of the Boyer-Moor algorithm, which is one of the fastest algorithms for string mathcing available in the literature. The aim of the parallel version of WORDUP presented here is to speed up the computational time and allow the analysis of a greater set of longer nucleotide sequences, which is usually impratical with sequential algorithms.I documenti in IRIS sono protetti da copyright e tutti i diritti sono riservati, salvo diversa indicazione.
