A user-programmable vertex engine
Proceedings of the 28th annual conference on Computer graphics and interactive techniques
ICCD '02 Proceedings of the 2002 IEEE International Conference on Computer Design: VLSI in Computers and Processors (ICCD'02)
Brook for GPUs: stream computing on graphics hardware
ACM SIGGRAPH 2004 Papers
Merrimac: Supercomputing with Streams
Proceedings of the 2003 ACM/IEEE conference on Supercomputing
Understanding the efficiency of GPU algorithms for matrix-matrix multiplication
Proceedings of the ACM SIGGRAPH/EUROGRAPHICS conference on Graphics hardware
Accelerator design for protein sequence HMM search
Proceedings of the 20th annual international conference on Supercomputing
Sequoia: programming the memory hierarchy
Proceedings of the 2006 ACM/IEEE conference on Supercomputing
Sequoia: programming the memory hierarchy
Proceedings of the 2006 ACM/IEEE conference on Supercomputing
Compilation for explicitly managed memory hierarchies
Proceedings of the 12th ACM SIGPLAN symposium on Principles and practice of parallel programming
MPI-HMMER-Boost: Distributed FPGA Acceleration
Journal of VLSI Signal Processing Systems
Journal of VLSI Signal Processing Systems
Streaming Algorithms for Biological Sequence Alignment on GPUs
IEEE Transactions on Parallel and Distributed Systems
A portable runtime interface for multi-level memory hierarchies
Proceedings of the 13th ACM SIGPLAN Symposium on Principles and practice of parallel programming
Application development on hybrid systems
Proceedings of the 2007 ACM/IEEE conference on Supercomputing
Visions for application development on hybrid computing systems
Parallel Computing
Adapting a message-driven parallel application to GPU-accelerated clusters
Proceedings of the 2008 ACM/IEEE conference on Supercomputing
Integrating FPGA acceleration into HMMer
Parallel Computing
HSP-HMMER: a tool for protein domain identification on a large scale
Proceedings of the 2009 ACM symposium on Applied Computing
Hardware Acceleration of HMMER on FPGAs
Journal of Signal Processing Systems
Molecular dynamics simulations on commodity GPUs with CUDA
HiPC'07 Proceedings of the 14th international conference on High performance computing
Accelerating HMMER on GPUs by implementing hybrid data and task parallelism
Proceedings of the First ACM International Conference on Bioinformatics and Computational Biology
A HMMER hardware accelerator using divergences
Proceedings of the Conference on Design, Automation and Test in Europe
Bio-sequence database scanning on a GPU
IPDPS'06 Proceedings of the 20th international conference on Parallel and distributed processing
Automatic CPU-GPU communication management and optimization
Proceedings of the 32nd ACM SIGPLAN conference on Programming language design and implementation
Autotuned parallel I/O for highly scalable biosequence analysis
Proceedings of the 2011 TeraGrid Conference: Extreme Digital Discovery
GPU-ClustalW: using graphics hardware to accelerate multiple sequence alignment
HiPC'06 Proceedings of the 13th international conference on High Performance Computing
Exploring the limits of GPGPU scheduling in control flow bound applications
ACM Transactions on Architecture and Code Optimization (TACO) - HIPEAC Papers
GPU accelerated smith-waterman
ICCS'06 Proceedings of the 6th international conference on Computational Science - Volume Part IV
Accelerating the viterbi algorithm for profile hidden markov models using reconfigurable hardware
ICCS'06 Proceedings of the 6th international conference on Computational Science - Volume Part I
A new parallel method of smith-waterman algorithm on a heterogeneous platform
ICA3PP'10 Proceedings of the 10th international conference on Algorithms and Architectures for Parallel Processing - Volume Part I
Dynamically managed data for CPU-GPU architectures
Proceedings of the Tenth International Symposium on Code Generation and Optimization
A protein sequence analysis hardware accelerator based on divergences
International Journal of Reconfigurable Computing - Special issue on High-Performance Reconfigurable Computing
A fast implementation of the octagon abstract domain on graphics hardware
SAS'07 Proceedings of the 14th international conference on Static Analysis
Multi-parallel prefiltering on the convey HC-1 for supporting homology detection
Proceedings of the 20th European MPI Users' Group Meeting
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The proliferation of biological sequence data has motivated the need for an extremely fast probabilistic sequence search. One method for performing this search involves evaluating the Viterbi probability of a hidden Markov model (HMM) of a desired sequence family for each sequence in a protein database. However, one of the difficulties with current implementations is the time required to search large databases. Many current and upcoming architectures offering large amounts of compute power are designed with data-parallel execution and streaming in mind. We present a streaming algorithm for evaluating an HMM's Viterbi probability and refine it for the specific HMM used in biological sequence search. We implement our streaming algorithm in the Brook language, allowing us to execute the algorithm on graphics processors. We demonstrate that this streaming algorithm on graphics processors can outperform available CPU implementations. We also demonstrate this implementation running on a 16 node graphics cluster.