Implementing Parallel Hmm-pfam on the EARTH Multithreaded Architecture
CSB '03 Proceedings of the IEEE Computer Society Conference on Bioinformatics
The UCSC Kestrel Parallel Processor
IEEE Transactions on Parallel and Distributed Systems
Exploiting Coarse-Grained Parallelism to Accelerate Protein Motif Finding with a Network Processor
Proceedings of the 14th International Conference on Parallel Architectures and Compilation Techniques
ClawHMMER: A Streaming HMMer-Search Implementatio
SC '05 Proceedings of the 2005 ACM/IEEE conference on Supercomputing
Accelerating the HMMER Sequence Analysis Suite Using Conventional Processors
AINA '06 Proceedings of the 20th International Conference on Advanced Information Networking and Applications - Volume 01
Accelerator design for protein sequence HMM search
Proceedings of the 20th annual international conference on Supercomputing
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
Error bounds for convolutional codes and an asymptotically optimum decoding algorithm
IEEE Transactions on Information Theory
A Massively Parallel Architecture for Bioinformatics
ICCS '09 Proceedings of the 9th International Conference on Computational Science: Part I
Accelerating HMMER on GPUs by implementing hybrid data and task parallelism
Proceedings of the First ACM International Conference on Bioinformatics and Computational Biology
Accelerating ncRNA homology search with FPGAs
Proceedings of the ACM/SIGDA international symposium on Field programmable gate arrays
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HMMer is a commonly used package for biological sequence database searching with profile hidden Markov model (HMMs). It allows researchers to compare HMMs to sequence databases or sequences to HMM databases. However, such searches often take many hours on traditional computer architectures. These runtime requirements are likely to become even more severe due to the rapid growth in size of both sequence and model databases. We present a new reconfigurable architecture to accelerate the two HMMer database search procedures hmmsearch and hmmpfam. It is described how this leads to significant runtime savings on off-the-shelf field-programmable gate arrays (FPGAs).