Paper Info
Title
MSA-GPU: Exact Multiple Sequence Alignment Using GPU
Abstract
In this paper, we propose and evaluate MSA-GPU, a solution to implement the exact Multiple Sequence Alignment algorithm in Graphics Processing Units (GPUs). In our solution, we use the Carrillo-Lipman upper and lower bounds to reduce the amount of computation. We propose a fine-grained strategy to explore the search space by using 2D projections. The results were obtained with a GTX 580 NVidia GPU comparing sets of 3 sequences (real and synthetic). We show that, for sequences with medium/low similarity, our GPU approach is able to outperform the MSA 2.0 CPU program, achieving a speedup of 8.6x.
Year
DOI
Venue
2013
10.1007/978-3-319-02624-4_5
BSB
Field
DocType
Volume
Graphics,Computer science,Upper and lower bounds,Parallel computing,SIMD,Multiple sequence alignment,Speedup,Computation
Conference
8213
ISSN
Citations 
PageRank 
0302-9743
4
0.46
References 
Authors
10
2
Name
Order
Citations
PageRank
Daniel Sundfeld151.87
Alba Cristina Magalhaes Alves De Melo225333.90