• Search Research Projects
  • Search Researchers
  • How to Use
  1. Back to previous page

Faster genome mapping method using 4-ary Perfect Linear Code

Research Project

Project/Area Number 24650155
Research Category

Grant-in-Aid for Challenging Exploratory Research

Allocation TypeMulti-year Fund
Research Field Bioinformatics/Life informatics
Research InstitutionOsaka University

Principal Investigator

takenaka yoichi  大阪大学, 情報科学研究科, 准教授 (00324830)

Project Period (FY) 2012-04-01 – 2016-03-31
Project Status Completed (Fiscal Year 2015)
Budget Amount *help
¥3,770,000 (Direct Cost: ¥2,900,000、Indirect Cost: ¥870,000)
Fiscal Year 2014: ¥1,560,000 (Direct Cost: ¥1,200,000、Indirect Cost: ¥360,000)
Fiscal Year 2013: ¥1,430,000 (Direct Cost: ¥1,100,000、Indirect Cost: ¥330,000)
Fiscal Year 2012: ¥780,000 (Direct Cost: ¥600,000、Indirect Cost: ¥180,000)
Keywordsゲノム / 完全線形符号 / 次世代シークエンサー / DNA配列 / ガロア拡大体 / ゲノムマッピング / アライメント
Outline of Final Research Achievements

The emerging of the next generation DNA sequencers enables us to get an extraordinary amount of DNA short sequences and read their bases. The data size comes bigger and bigger year by year and the increase ratio overwhelms the Moore’s law. This requires new algorithms and mechanism to manipulate the short read faster. This research proposed that 4-ary perfect linear code meets the demand. The DNA sequences are coded to one of the code words of the perfect linear code and we proved that it reduces the search space when we try to find DNA subsequences that is one mismatch from the query DNA sequence. Then we have shown that the perfect linear code is useful to genome mapping and metagenome analyses.

Report

(5 results)
  • 2015 Annual Research Report   Final Research Report ( PDF )
  • 2014 Research-status Report
  • 2013 Research-status Report
  • 2012 Research-status Report
  • Research Products

    (16 results)

All 2015 2014 2013 2012 Other

All Journal Article (3 results) (of which Peer Reviewed: 3 results,  Open Access: 1 results) Presentation (13 results)

  • [Journal Article] Metagenome fragment classification based on multiple motif-occurrence profiles2014

    • Author(s)
      Naoki Matsushita, Shigeto Seno, Yoichi Takenaka, Hideo Matsuda
    • Journal Title

      PeerJ

      Volume: 2: e559 Pages: 1-13

    • DOI

      10.7717/peerj.559

    • Related Report
      2014 Research-status Report
    • Peer Reviewed / Open Access
  • [Journal Article] An estimation method for a cellular-state-specific gene regulatory network along tree-structured gene expression profiles2013

    • Author(s)
      Ryo Araki, Shigeto Seno, Yoichi Takenaka, Hideo Matsuda
    • Journal Title

      Gene

      Volume: Vol.518 Issue: 1 Pages: 17-25

    • DOI

      10.1016/j.gene.2012.11.090

    • Related Report
      2013 Research-status Report
    • Peer Reviewed
  • [Journal Article] 複数時系列遺伝子発現プロファイルを利用した遺伝子制御ネットワーク推定の精度向上手法2013

    • Author(s)
      渡邉之人, 瀬尾茂人, 竹中要一, 松田秀雄
    • Journal Title

      情報処理学会論文誌 数理モデル化と応用

      Volume: 6 Pages: 151-162

    • NAID

      110009550160

    • Related Report
      2013 Research-status Report
    • Peer Reviewed
  • [Presentation] 共通k-mer種別数に基づくメタゲノム分類手法2015

    • Author(s)
      吉田拓真, 瀬尾茂人, 竹中要一, 松田秀雄
    • Organizer
      第4回NGS現場の会
    • Place of Presentation
      つくば国際会議場 (茨城県つくば市)
    • Year and Date
      2015-07-01
    • Related Report
      2015 Annual Research Report
  • [Presentation] Chronological analysis of regulatory strength on gene regulatory networks2014

    • Author(s)
      Yoichi Takenaka, Shigeto Seno and Hideo Matsuda
    • Organizer
      ECCB 2014
    • Place of Presentation
      Boston
    • Year and Date
      2014-07-07 – 2014-07-10
    • Related Report
      2014 Research-status Report
  • [Presentation] Gene Set Enrichment Analysis for a Long Time Series Gene Expression Profile2013

    • Author(s)
      Yuta Okuma, Shigeto Seno, Yoichi Takenaka, Hideo Matsuda
    • Organizer
      The 2013 World Congress in Computer Science Computer Engineering and Applied Computing (BIOCOMP'13)
    • Place of Presentation
      Las Vegas,USA
    • Related Report
      2013 Research-status Report
  • [Presentation] A Method of Sequence Analysis for High-Throughput Sequencer Data Based on Shifted Short Read Clustering2013

    • Author(s)
      Kensuke Suzuki, Daisuke Ueta, Shigeto Seno, Yoichi Takenaka
    • Organizer
      The 2013 World Congress in Computer Science Computer Engineering and Applied Computing (BIOCOMP'13)
    • Place of Presentation
      Las Vegas USA
    • Related Report
      2013 Research-status Report
  • [Presentation] Reconstruction of Dynamic Gene Regulatory Networks for Cell Differentiation by Separation of Time-course Data2013

    • Author(s)
      Tomoyoshi Nakayama, Hiromi Daiyasu, Shigeto Seno, Yoichi Takenaka
    • Organizer
      The 2013 World Congress in Computer Science Computer Engineering and Applied Computing (BIOCOMP'13)
    • Place of Presentation
      Las Vegas, USA
    • Related Report
      2013 Research-status Report
  • [Presentation] Integrative prediction of miRNA-mRNA interactions from high-throughput sequencing data2013

    • Author(s)
      Tomoshige Ohno, Shigeto Seno, Hiromi Daiyasu, Yoichi Takenaka, Hideo Matsuda
    • Organizer
      RECOMB/ISCB Conference on Regulatory and Systems Genomics, with DREAM Challenges 2013
    • Place of Presentation
      Toronto, CANADA
    • Related Report
      2013 Research-status Report
  • [Presentation] Multiplication of Motif Occurrence Profiles for Metagenome Fragment Classification2013

    • Author(s)
      Naoki Matsushita, Hiromi Daiyasu, Shigeto Seno, Yoichi Takenaka, Hideo Matsuda
    • Organizer
      35th Annual International IEEE EMBS Conference
    • Place of Presentation
      Osaka JAPAN
    • Related Report
      2013 Research-status Report
  • [Presentation] Gene Set Enrichment Analysis for Time-Series Gene Expression Profile2013

    • Author(s)
      Yuta Okuma, Shigeto Seno, Yoichi Takenaka, Hideo Matsuda
    • Organizer
      35th Annual International IEEE EMBS Conference
    • Place of Presentation
      Osaka JAPAN
    • Related Report
      2013 Research-status Report
  • [Presentation] 長いリードを計算機で扱うのに完全線形符号が効果的だと思うのです2013

    • Author(s)
      竹中要一, 瀬尾茂人, 松田秀雄
    • Organizer
      第三回NGS現場の会
    • Place of Presentation
      Kobe JAPAN
    • Related Report
      2013 Research-status Report
  • [Presentation] 多次元尺度構成法によるリード分類結果の視覚化2013

    • Author(s)
      吉田拓真, 竹中要一, 瀬尾茂人, 松田秀雄
    • Organizer
      第三回NGS現場の会
    • Place of Presentation
      Kobe JAPAN
    • Related Report
      2013 Research-status Report
  • [Presentation] Perfect linear code reduces the solution space of genome mapping from 1+3n to 22.2 + 0.00879n to find one-mismatch for n-mer short reads2012

    • Author(s)
      Yoichi Takenaka
    • Organizer
      Special Interest Group Meetings of High-Throughput Sequencing at International Conference on Intelligent Systems for Molecular Biology (ISMB2012)
    • Place of Presentation
      CA USA
    • Related Report
      2012 Research-status Report
  • [Presentation] All the 1+3n one-mismatch sequences of n-mer DNA are involved in 22.2+0.00879n strings of Perfect Linear Code words on DNA

    • Author(s)
      Yoichi Takenaka
    • Organizer
      International Conference on Intelligent Systems for Molecular Biology (ISMB2012)
    • Place of Presentation
      CA USA
    • Related Report
      2012 Research-status Report
  • [Presentation] ゲノムマッピング: Burrows-Wheeler transformの次のアルゴリズム

    • Author(s)
      竹中要一
    • Organizer
      NGS現場の会 第二回研究会
    • Place of Presentation
      大阪
    • Related Report
      2012 Research-status Report

URL: 

Published: 2013-05-31   Modified: 2019-07-29  

Information User Guide FAQ News Terms of Use Attribution of KAKENHI

Powered by NII kakenhi