Paper Info
Title
Exact Parallel Alignment Of Megabase Genomic Sequences With Tunable Work Distribution
Abstract
Sequence Alignment is a. basic operation in Bioinformatics that is performed thousands of times, on daily basis. The exact methods for pairwise alignment have quadratic time complexity. For this reason, heuristic methods such as BLAST are widely used. To obtain exact results faster, parallel strategies have been proposed but most of them fail to align huge biological sequences. This happens because not only the quadratic time must be considered but also the space should be reduced. In this paper, we evaluate the performance of Z-align, a parallel exact strategy that runs in user-restricted memory space. Also, we propose and evaluate a tunable work distribution mechanism. The results obtained in two clusters show that two sequences of size 24MBP (Mega Base Pairs) and 23MBP, respectively, were successfully aligned with Z-align. Also, in order to align two 3MBP sequences, a speedup of 34.35 was achieved for 64 processors. The evaluation of our work distribution mechanism shows that the execution times can be sensibly reduced when appropriate parameters are chosen. Finally, when comparing Z-align with BLAST, it is clear that, in many cases, Z-align is able to produce alignments with higher score.
Year
DOI
Venue
2012
10.1142/S0129054112400205
INTERNATIONAL JOURNAL OF FOUNDATIONS OF COMPUTER SCIENCE
Keywords
Field
DocType
Parallel algorithms, dynamic programming
Sequence alignment,Dynamic programming,Pairwise comparison,Cluster (physics),Heuristic,Combinatorics,Parallel algorithm,Time complexity,Mathematics,Speedup
Journal
Volume
Issue
ISSN
23
2
0129-0541
Citations 
PageRank 
References 
2
0.37
3
Authors
5
Name
Order
Citations
PageRank
Azzedine Boukerche14301418.60
Rodolfo Bezerra Batista2283.31
Alba Cristina Magalhaes Alves De Melo325333.90
Felipe Brandt Scarel420.37
Lavir Antonio Bahia Carvalho de Souza520.37