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Design and Implementation of high-performance sequence analysis environment using GPGPU

Research Project

Project/Area Number 21510217
Research Category

Grant-in-Aid for Scientific Research (C)

Allocation TypeSingle-year Grants
Section一般
Research Field ゲノム情報科学
Research InstitutionNational Institute of Agrobiological Sciences

Principal Investigator

SUETSUGU Yoshitaka  独立行政法人農業生物資源研究所, 昆虫ゲノム研究ユニット, 主任研究員 (80533471)

Co-Investigator(Kenkyū-buntansha) FUNAHASHI Akira  慶應義塾大学, 理工学部・生命情報学科, 准教授 (70324548)
Project Period (FY) 2009 – 2011
Project Status Completed (Fiscal Year 2011)
Budget Amount *help
¥3,510,000 (Direct Cost: ¥2,700,000、Indirect Cost: ¥810,000)
Fiscal Year 2011: ¥910,000 (Direct Cost: ¥700,000、Indirect Cost: ¥210,000)
Fiscal Year 2010: ¥650,000 (Direct Cost: ¥500,000、Indirect Cost: ¥150,000)
Fiscal Year 2009: ¥1,950,000 (Direct Cost: ¥1,500,000、Indirect Cost: ¥450,000)
Keywords情報工学 / 配列解析 / 並列処理 / ゲノム / GPGPU / バイオインフォマティクス
Research Abstract

Since the emergence of high-throughput sequencing platform, the cost for both experimental and time were much reduced for DNA sequencing. This makes easy to produce enormous amount of DNA data. As the result, analyzing huge sequence database has become a next target to find an e & cient solution. To overcome this problem, we applied General Purpose computation on Graphic Processing Unit(GPGPU) for sequence analysis. We implemented several algorithms including Smith-Waterman algorithm based on GPGPU. The GPU-based programs showed higher performance compared to CPU-based ones.

Report

(4 results)
  • 2011 Annual Research Report   Final Research Report ( PDF )
  • 2010 Annual Research Report
  • 2009 Annual Research Report
  • Research Products

    (4 results)

All 2010 2009

All Presentation (4 results)

  • [Presentation] MULTI-GPUsによる高速配列解析環境の構築2010

    • Author(s)
      平田一樹,太田信行,上樂明也,広井賀子,舟橋啓,末次克行
    • Organizer
      第33回日本分子生物学会年会・第83回日本生化学会大会合同大会
    • Place of Presentation
      神戸市
    • Year and Date
      2010-12-09
    • Related Report
      2011 Final Research Report
  • [Presentation] MULTI-GPUsによる高速配列解析環境の構築2010

    • Author(s)
      平田一樹, 太田信行, 上樂明也, 広井賀子, 舟橋啓, 末次克行
    • Organizer
      第33回日本分子生物学会年会・第83回日本生化学会大会 合同大会
    • Place of Presentation
      神戸ポートアイランド(兵庫県)
    • Year and Date
      2010-12-09
    • Related Report
      2010 Annual Research Report
  • [Presentation] Design and Implementation of high-performance sequence analysis environment using GPGPU2009

    • Author(s)
      Kazuki Hirata, Nobuyuki Ohta, Noriko Hiroi, Akira Funahashi, Yoshitaka Suetsugu
    • Organizer
      第32回日本分子生物学会年会
    • Place of Presentation
      横浜市
    • Year and Date
      2009-12-11
    • Related Report
      2011 Final Research Report
  • [Presentation] Design and Implementation of high-performance sequence analysis environment using GPGPU2009

    • Author(s)
      Kazuki Hirata, Nobuyuki Ohta, Noriko Hiroi, Akira Funahashi, Yoshitaka Suetsugu
    • Organizer
      第32回日本分子生物学会年会
    • Place of Presentation
      パシフィコ横浜(神奈川県)
    • Year and Date
      2009-12-11
    • Related Report
      2009 Annual Research Report

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Published: 2009-04-01   Modified: 2016-04-21  

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