Presentation 2010-09-16
Accelerating HMMER search using FPGA Grid
Toyokazu TAKAGI, Tutomu MARUYAMA,
PDF Download Page PDF download Page Link
Abstract(in Japanese) (See Japanese page)
Abstract(in English) HMMER is one of the most used software tools for sensitive profile HMM (Hidden Markov Model) searches of biological sequence databases. HMMER can be accelerated by comparing a profile HMM with N sequences in parallel using a computing grid with N nodes. HMMER is, however, still a cpu-intensive program. In HMMER, the Viterbi algorithm, which is a quadratic dynamic programming algorithm, is used to align a profile HMM and a sequence. Using a dedicated hardware, the search by the Viterbi algorithm can be accelerated by processing several nodes in the search space in parallel. In this paper, we describe an approach for accelerating HMMER search using an FPGA grid.
Keyword(in Japanese) (See Japanese page)
Keyword(in English) FPGA / HMMER / profile HMM / parallel computation / grid computing
Paper # RECONF2010-23
Date of Issue

Conference Information
Committee RECONF
Conference Date 2010/9/9(1days)
Place (in Japanese) (See Japanese page)
Place (in English)
Topics (in Japanese) (See Japanese page)
Topics (in English)
Vice Chair

Paper Information
Registration To Reconfigurable Systems (RECONF)
Language JPN
Title (in Japanese) (See Japanese page)
Sub Title (in Japanese) (See Japanese page)
Title (in English) Accelerating HMMER search using FPGA Grid
Sub Title (in English)
Keyword(1) FPGA
Keyword(2) HMMER
Keyword(3) profile HMM
Keyword(4) parallel computation
Keyword(5) grid computing
1st Author's Name Toyokazu TAKAGI
1st Author's Affiliation Systems and Information Engineering, University of Tsukuba()
2nd Author's Name Tutomu MARUYAMA
2nd Author's Affiliation Systems and Information Engineering, University of Tsukuba
Date 2010-09-16
Paper # RECONF2010-23
Volume (vol) vol.110
Number (no) 204
Page pp.pp.-
#Pages 6
Date of Issue