Faster genome mapping method using 4-ary Perfect Linear Code

• Project/Area Number: 24650155
• Research Category: Grant-in-Aid for Challenging Exploratory Research
• Allocation Type: Multi-year Fund
• Research Field: Bioinformatics/Life informatics
• Research Institution: Osaka 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: ¥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.

Research Products

• [Journal Article] Metagenome fragment classification based on multiple motif-occurrence profiles (2014)
  • Author(s): Naoki Matsushita, Shigeto Seno, Yoichi Takenaka, Hideo Matsuda
  • Journal Title: PeerJ Volume: 2: e559 Pages: 1-13
  • DOI: 10.7717/peerj.559
  • Peer Reviewed / Open Access
• [Journal Article] An estimation method for a cellular-state-specific gene regulatory network along tree-structured gene expression profiles (2013)
  • 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
  • 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
  • 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
• [Presentation] Chronological analysis of regulatory strength on gene regulatory networks (2014)
  • 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
• [Presentation] Gene Set Enrichment Analysis for a Long Time Series Gene Expression Profile (2013)
  • 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
• [Presentation] A Method of Sequence Analysis for High-Throughput Sequencer Data Based on Shifted Short Read Clustering (2013)
  • 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
• [Presentation] Reconstruction of Dynamic Gene Regulatory Networks for Cell Differentiation by Separation of Time-course Data (2013)
  • 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
• [Presentation] Integrative prediction of miRNA-mRNA interactions from high-throughput sequencing data (2013)
  • 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
• [Presentation] Multiplication of Motif Occurrence Profiles for Metagenome Fragment Classification (2013)
  • Author(s): Naoki Matsushita, Hiromi Daiyasu, Shigeto Seno, Yoichi Takenaka, Hideo Matsuda
  • Organizer: 35th Annual International IEEE EMBS Conference
  • Place of Presentation: Osaka JAPAN
• [Presentation] Gene Set Enrichment Analysis for Time-Series Gene Expression Profile (2013)
  • Author(s): Yuta Okuma, Shigeto Seno, Yoichi Takenaka, Hideo Matsuda
  • Organizer: 35th Annual International IEEE EMBS Conference
  • Place of Presentation: Osaka JAPAN
• [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
• [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
• [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 reads (2012)
  • 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
• [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
• [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