Hardware Acceleration of HMMER on FPGAs
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 para...
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Published in | Journal of signal processing systems Vol. 58; no. 1; pp. 53 - 67 |
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Main Authors | , |
Format | Journal Article |
Language | English |
Published |
Boston
Springer US
2010
Springer |
Subjects | |
Online Access | Get full text |
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Summary: | 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. |
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Bibliography: | ObjectType-Article-2 SourceType-Scholarly Journals-1 ObjectType-Feature-1 content type line 23 |
ISSN: | 1939-8018 1939-8115 |
DOI: | 10.1007/s11265-008-0262-y |