Skip Navigation

This Article
Right arrow Full Text (Print PDF)
Right arrow Alert me when this article is cited
Right arrow Alert me if a correction is posted
Services
Right arrow Email this article to a friend
Right arrow Similar articles in this journal
Right arrow Alert me to new issues of the journal
Right arrow Add to My Personal Archive
Right arrow Download to citation manager
Right arrowRequest Permissions
Google Scholar
Right arrow Articles by Liuni, S.
Right arrow Articles by Distante, A.
Right arrow Search for Related Content
PubMed
Right arrow Articles by Liuni, S.
Right arrow Articles by Distante, A.
Social Bookmarking
Add to CiteULike   Add to Connotea   Add to Del.icio.us  
What's this?

© Oxford University Press

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

Sabino Liuni , Nicola Prunella 1, Graziano Pesole 2, Tiziana D'Orazio 3, Ettore Stella 3 and Arcangelo Distante 3

CSMME-CNR
1CSMME-CNR Bari, Italy
2Dipartimento di Biochimica e Biologia Molecolare Bari, Italy
3Istituto Elaborazione Segnali ed Immagini Bari, Italy

The development of new techniques in sequencing nucleic acids has produced 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 sequences. WORDUP implements an efficient method to identify the presence of statistically significant oligomers in a nonhomologous group of sequences. It is based on a modified version of the Boyer-Moore algorithm, which is one of the fastest algorithms for string matching 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 impractical with sequential algorithms.

Received on March 13, 1993; accepted on August 6, 1993

Add to CiteULike CiteULike   Add to Connotea Connotea   Add to Del.icio.us Del.icio.us    What's this?




Disclaimer:
Please note that abstracts for content published before 1996 were created through digital scanning and may therefore not exactly replicate the text of the original print issues. All efforts have been made to ensure accuracy, but the Publisher will not be held responsible for any remaining inaccuracies. If you require any further clarification, please contact our Customer Services Department.