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2005
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ClawHMMER: A Streaming HMMer-Search Implementation

9 years 4 months ago
ClawHMMER: A Streaming HMMer-Search Implementation
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 ...
Daniel Reiter Horn, Mike Houston, Pat Hanrahan
Added 26 Jun 2010
Updated 26 Jun 2010
Type Conference
Year 2005
Where SC
Authors Daniel Reiter Horn, Mike Houston, Pat Hanrahan
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