Abstract

Comparison between biosequences and probabilistic models is an increasingly important part of modern DNA and protein sequence analysis. The large and growing number of such models in today's databases demands computational approaches to searching these databases faster, while maintaining high sensitivity to biologically meaningful similarities. This work describes an FPGA-based accelerator for comparing proteins to hidden Markov models of the type used to represent protein motifs in the popular HM-MER motif finder. Our engine combines a systolic array design with enhancements to pipeline the complex Viterbi calculation that forms the core of the comparison, and to support coarse-grained parallelism and streaming of multiple sequences within one FPGA. Performance estimates based on a functioning VHDL realisation of our design show a 190 times speedup over the same computation in optimised software on a modern general-purpose CPU.

Keywords

Computer scienceField-programmable gate arraySpeedupViterbi algorithmHidden Markov modelPipeline (software)VHDLParallel computingProbabilistic logicComputer architectureArtificial intelligenceEmbedded systemProgramming language

Affiliated Institutions

Related Publications

Accelerated Profile HMM Searches

Sean R. Eddy

Profile hidden Markov models (profile HMMs) and probabilistic inference methods have made important contributions to the theory of sequence database homology search. However, pr...

2011 PLoS Computational Biology 6891 citations

Profile hidden Markov models.

Sean R. Eddy

Abstract The recent literature on profile hidden Markov model (profile HMM) methods and software is reviewed. Profile HMMs turn a multiple sequence alignment into a position-spe...

1998 Bioinformatics 5657 citations

Publication Info

Year
2007
Type
article
Volume
3991
Pages
1-8
Citations
24
Access
Closed

External Links

Download PDF (Free) View on DOI.org Semantic Scholar

Social Impact

Altmetric
PlumX Metrics

Social media, news, blog, policy document mentions

Citation Metrics

24
OpenAlex
3
Influential
16
CrossRef

Cite This

Arpith C. Jacob, Joseph M. Lancaster, Jeremy Buhler et al. (2007). Preliminary results in accelerating profile HMM search on FPGAs. 2007 IEEE International Parallel and Distributed Processing Symposium , 3991 , 1-8. https://doi.org/10.1109/ipdps.2007.370447

Identifiers

DOI
10.1109/ipdps.2007.370447

Data Quality

Data completeness: 81%