Paper Info
Title
A parallel strategy for biological sequence alignment in restricted memory space
Abstract
Recently, many organisms had their DNA entirely sequenced, and this reality presents the need for aligning long DNA sequences, which is a challenging task due to its high demands for computational power and memory. The algorithm proposed by Smith-Waterman (SW) is an exact method that obtains optimal local alignments in quadratic space and time. For long sequences, quadratic complexity makes the use of this algorithm impractical. In this scenario, parallel computing is a very attractive alternative. In this paper, we propose and evaluate z-align, a parallel exact strategy based on the divergence concept to locally align long biological sequences using an affine gap function. Z-align runs in limited memory space, where the amount of memory used can be defined by the user. The results collected in a cluster with 16 processors presented very good speedups for long real DNA sequences. With z-align, we were able to compare up to 3MBP (mega base-pairs) DNA sequences. As far as we know, this is the first time 3MBP sequences are compared with an affine gap exact variation of the SW algorithm. Also, by comparing the results obtained with z-align and the popular BLAST tool, it is clear that z-align is able to produce longer and more significant alignments.
Year
DOI
Venue
2008
10.1016/j.jpdc.2007.08.007
J. Parallel Distrib. Comput.
Keywords
Field
DocType
exact variation,dna sequence,restricted memory space,exact method,long dna sequence,biological sequence alignment,parallel strategy,long real dna sequence,limited memory space,sw algorithm,align long biological sequence,long sequence,parallel exact strategy,sequence alignment,high performance computing,dna sequencing,local alignment,base pair,parallel computer
Sequence alignment,Affine transformation,Supercomputer,Parallel algorithm,Computer science,Parallel computing,Spacetime,Quadratic equation,Algorithm,Mega-,Biological sequence alignment
Journal
Volume
Issue
ISSN
68
4
Journal of Parallel and Distributed Computing
Citations 
PageRank 
References 
15
0.98
8
Authors
3
Name
Order
Citations
PageRank
Rodolfo Bezerra Batista1283.31
Azzedine Boukerche24301418.60
Alba Cristina Magalhaes Alves De Melo325333.90