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

Author

Liuni, S. ; Prunella, N. ; Pesole, G. ; D´Orazio, T. ; Stella, E. ; Distante, A.

Author_Institution

CSMME-CNR, Bari, Italy

fYear

1993

Firstpage

605

Abstract

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.

Keywords

DNA; biology computing; parallel algorithms; pattern recognition; statistics; DNA sequences; MEIKO parallel machines; WORDUP; computational time; nonhomologous group; nucleotide sequences; oligomers; parallel algorithm; performance; sequence matching; statistically significant patterns; Algorithm design and analysis; Biological information theory; Biology computing; Computational biology; Concurrent computing; DNA computing; Genetics; Parallel algorithms; Parallel machines; Proteins; Sequences; Testing;

fLanguage

English

Publisher

ieee

Conference_Titel

System Sciences, 1993, Proceeding of the Twenty-Sixth Hawaii International Conference on

Print_ISBN

0-8186-3230-5

Type

conf

DOI

10.1109/HICSS.1993.270680

Filename

270680