Paper Info
Title
CUDAlign 4.0: Incremental Speculative Traceback for Exact Chromosome-Wide Alignment in GPU Clusters.
Abstract
This paper proposes and evaluates CUDAlign 4.0, a parallel strategy to obtain the optimal alignment of huge DNA sequences in multi-GPU platforms, using the exact Smith–Waterman (SW) algorithm. In the first phase of CUDAlign 4.0, a huge Dynamic Programming (DP) matrix is computed by multiple GPUs, which asynchronously communicate border elements to the right neighbor in order to find the optimal sc...
Year
DOI
Venue
2016
10.1109/TPDS.2016.2515597
IEEE Transactions on Parallel and Distributed Systems
Keywords
Field
DocType
Graphics processing units,DNA,Bioinformatics,Heuristic algorithms,Genomics,Biological cells,Dynamic programming
Cluster (physics),Dynamic programming,Data dependency,Hit ratio,Computer science,Matrix (mathematics),Parallel algorithm,Parallel computing,Algorithm,Distributed computing,Scalability
Journal
Volume
Issue
ISSN
27
10
1045-9219
Citations 
PageRank 
References 
18
0.79
19
Authors
6
Name
Order
Citations
PageRank
Edans Sandes11298.94
Guillermo Miranda2261.62
Xavier Martorell31470125.40
Eduard Ayguadé42406216.00
George Teodoro515022.18
Alba Cristina Magalhaes Alves De Melo625333.90