Partitioning and Mapping Algorithms into Fixed Size Systolic Arrays
IEEE Transactions on Computers
Some efficient solutions to the affine scheduling problem: I. One-dimensional time
International Journal of Parallel Programming
Combined instruction and loop parallelism in array synthesis for FPGAs
Proceedings of the 14th international symposium on Systems synthesis
Constructing and exploiting linear schedules with prescribed parallelism
ACM Transactions on Design Automation of Electronic Systems (TODAES)
Automatic synthesis of systolic arrays from uniform recurrent equations
ISCA '84 Proceedings of the 11th annual international symposium on Computer architecture
Hyper customized processors for bio-sequence database scanning on FPGAs
Proceedings of the 2005 ACM/SIGDA 13th international symposium on Field-programmable gate arrays
Cluster of re-configurable nodes for scanning large genomic banks
Parallel Computing
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
A Reconfigurable Index FLASH Memory tailored to Seed-Based Genomic Sequence Comparison Algorithms
Journal of VLSI Signal Processing Systems
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
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We propose a new parallelization scheme for the hmmsearch function of the HMMER software, in order to target FPGA technology. hmmsearch is a very compute intensive software for biological sequence alignment, based on profile hidden Markov models. We derive a flexible, generic, scalable hardware parallel architecture which can accelerate the core of hmmsearch by nearly two orders of magnitude, without modifying the original algorithm of this software. Our derivation is based on the expression of the algorithm as a set of recurrence equations, and we show in a systematic way how a very efficient parallel version of the algorithm can be found by combining scheduling, projection, partitioning, pipelining and precision analysis. We present the performance of the implementation of this parallel algorithm on a FPGA platform.