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| Content Provider | IEEE Xplore Digital Library |
|---|---|
| Author | Yanteng Sun Peng Li Guochang Gu Yuan Wen Yuan Liu Dong Liu |
| Copyright Year | 2009 |
| Description | Author affiliation: College of Computer Science and Technology, Harbin Engineering University, China (Yanteng Sun; Peng Li; Guochang Gu; Yuan Wen) || Intel China Research Center, China (Yuan Liu; Dong Liu) |
| Abstract | HMMer is a widely-used bioinformatics software package that uses profile HMMs (Hidden Markov Models) to model the primary structure consensus of a family of protein or nucleic acid sequences. However, with the rapid growth of both sequence and model databases, it is more and more time-consuming to run HMMer on traditional computer architecture. In this paper, the computation kernel of HMMer, P7Viterbi, is selected to be accelerated by FPGA. There is an infrequent feedback loop in P7Viterbi to update the value of beginning state (B state), which limits further parallelization. Previous work either ignored the feedback loop or serialized the process, leading to loss of either precision or efficiency. Our proposed syslolic array based architecture with a parallel data providing unit can exploit maximum parallelism of the full version of P7Viterbi. The proposed architecture speculatively runs with fully parallelism assuming that the feedback loop does not take place. If the rare feedback case actually occurs, a rollback mechanism is used to ensure correctness. Results show that by using Xilinx Virtex-5 110T FPGA, the proposed architecture with 20 PEs can achieve about a 56.8 times speedup compared with that of Intel Core2 Duo 2.33GHz CPU. |
| Starting Page | 1 |
| Ending Page | 8 |
| File Size | 326401 |
| Page Count | 8 |
| File Format | |
| ISBN | 9781424437511 |
| ISSN | 15302075 |
| DOI | 10.1109/IPDPS.2009.5160927 |
| Language | English |
| Publisher | Institute of Electrical and Electronics Engineers, Inc. (IEEE) |
| Publisher Date | 2009-05-23 |
| Publisher Place | Italy |
| Access Restriction | Subscribed |
| Rights Holder | Institute of Electrical and Electronics Engineers, Inc. (IEEE) |
| Subject Keyword | Acceleration Field programmable gate arrays Systolic arrays Hidden Markov models Feedback loop Computer architecture Parallel processing Bioinformatics Software packages Proteins |
| Content Type | Text |
| Resource Type | Article |
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