Paper Info
Title
A Speculative HMMER Search Implementation on GPU
Abstract
Due to the exponentially growing bioinformatics databases and rapidly popular of GPU for general purpose computing, it is promising to employ GPU techniques to accelerate the sequence search process. Hmmsearch from HMMER bioinformatics software package is a wildly used software tool for sensitive profile HMM (Hidden Markov Model) searches of biological sequence databases. In this paper, we implement a speculative hmmsearch implementation on NVIDIA Fermi GPU and apply various optimizations to it. We test the enhancements in our GPU implementation in order to demonstrate the effectiveness of optimization strategies. Result shows that our speculative hmmsearch implementation achieves up to 6.5x speedup over previous fast single-threaded SSE implementation.
Year
DOI
Venue
2012
10.1109/IPDPSW.2012.91
IPDPS Workshops
Keywords
Field
DocType
hmmer bioinformatics software package,gpu technique,sequence search process,software tool,gpu implementation,biological sequence databases,bioinformatics databases,nvidia fermi gpu,speculative hmmer search implementation,speculative hmmsearch implementation,fast single-threaded sse implementation,database management systems,speculative,hidden markov model,registers,kernel,databases,hidden markov models,optimization,instruction sets,bioinformatics
Kernel (linear algebra),Software tool,General purpose computing,Computer science,Instruction set,Parallel computing,Software,Graphics processing unit,Hidden Markov model,Speedup
Conference
ISSN
Citations 
PageRank 
2164-7062
5
0.48
References 
Authors
14
7
Name
Order
Citations
PageRank
Xiaoqiang Li181.18
Wenting Han26112.61
Gu Liu3284.06
Hong An45824.15
Mu Xu5285.11
Wei Zhou619328.72
Qi Li750.82