Ultra-fast RNA structural alignments with pseudoknots

• Project/Area Number: 25330348
• Research Category: Grant-in-Aid for Scientific Research (C)
• Allocation Type: Multi-year Fund
• Section: 一般
• Research Field: Life / Health / Medical informatics
• Research Institution: Keio University
• Principal Investigator: Sato Kengo 慶應義塾大学, 理工学部(矢上), 講師 (20365472)
• Project Period (FY): 2013-04-01 – 2017-03-31
• Project Status: Completed (Fiscal Year 2016)
• Budget Amount: ¥4,810,000 (Direct Cost: ¥3,700,000、Indirect Cost: ¥1,110,000); Fiscal Year 2015: ¥1,300,000 (Direct Cost: ¥1,000,000、Indirect Cost: ¥300,000); Fiscal Year 2014: ¥2,080,000 (Direct Cost: ¥1,600,000、Indirect Cost: ¥480,000); Fiscal Year 2013: ¥1,430,000 (Direct Cost: ¥1,100,000、Indirect Cost: ¥330,000)
• Keywords: RNA二次構造 / 構造アラインメント / 期待精度最大化 / 双対分解 / 整数計画法 / マルチプルアラインメント / バイオインフォマティクス

Outline of Final Research Achievements

Despite the fact that RNA structural alignments have been studied for a long time, there is still a problem that the computational complexity is still large. For this reason, we cannot perform even a basic analysis of "comparing sequences" by exact methods for relatively long RNA sequences such as long non-coding RNAs and RNA viruses. In this research, we developed a fast and accurate method of calculating RNA structural alignments with consideration of complicated higher order structures such as pseudoknots by a novel algorithm based on maximizing the expected accuracy and the dual decomposition.

Research Products

• [Journal Article] An accessibility-incorporated method for accurate prediction of RNA-RNA interactions from sequence data (2017)
  • Author(s): Y. Kato, T. Mori, K. Sato, S. Maegawa, H. Hosokawa, T. Akutsu
  • Journal Title: Bioinformatics Volume: 33 Issue: 2 Pages: 202-209
  • DOI: 10.1093/bioinformatics/btw603
  • Peer Reviewed / Open Access
• [Journal Article] Rtools: a web server for various secondary structural analyses on single RNA sequences (2016)
  • Author(s): Hamada Michiaki, Ono Yukiteru, Kiryu Hisanori, Sato Kengo, Kato Yuki, Fukunaga Tsukasa, Mori Ryota, Asai Kiyosh
  • Journal Title: Nucleic Acids Research Volume: 44 Issue: W1 Pages: W302-W307
  • DOI: 10.1093/nar/gkw337
  • Peer Reviewed / Open Access / Int'l Joint Research / Acknowledgement Compliant
• [Journal Article] Prediction of Gene Structures from RNA-seq Data Using Dual Decomposition (2016)
  • Author(s): Inatsuki, T, Sato, K., Sakakibara, Y.
  • Journal Title: IPSJ Transactions on Bioinformatics Volume: 9 Issue: 0 Pages: 1-6
  • DOI: 10.2197/ipsjtbio.9.1
  • NAID: 130005139841
  • ISSN: 1882-6679
  • Peer Reviewed / Open Access / Acknowledgement Compliant
• [Journal Article] SHARAKU: An algorithm for aligning and clustering read mapping profiles of deep sequencing in non-coding RNA processing (2016)
  • Author(s): Tsuchiya, M., Amano, K., Abe, M., Seki, M., Hase, S., Sato, K., Sakakibara, Y.
  • Journal Title: Bioinformatics Volume: 32
  • Peer Reviewed / Open Access / Acknowledgement Compliant
• [Journal Article] Resequencing of the common marmoset genome improves genome assemblies and gene-coding sequence analysis (2015)
  • Author(s): Sato, K., Kuroki, Y., Kumita, W., Fujiyama, A., Toyoda, A., Kawai, J., Iriki, A., Sasaki, E., Okano, H., Sakakibara, Y.
  • Journal Title: Scientific Reports Volume: 5 Issue: 1 Pages: 16894-16894
  • DOI: 10.1038/srep16894
  • Peer Reviewed / Open Access
• [Journal Article] Whole-genome sequencing and comparative genome analysis of Bacillus subtilis strains isolated from non-salted fermented soybean foods (2015)
  • Author(s): Kamada, M., Hase, S., Fujii, K., Miyake, M., Sato, K., Kimura, K., Sakakibara, Y.
  • Journal Title: PLoS ONE Volume: 10 Issue: 10 Pages: e0141369-e0141369
  • DOI: 10.1371/journal.pone.0141369
  • Peer Reviewed / Open Access
• [Journal Article] A machine learning based approach to de novo sequencing of glycans from tandem mass spectrometry spectrum (2015)
  • Author(s): Kumozaki, S., Sato, K., Sakakibara, Y.
  • Journal Title: IEEE/ACM Transactions on Computatinal Biology and Bioinformatics Volume: 12
  • Peer Reviewed / Acknowledgement Compliant
• [Journal Article] MetaVelvet-SL: An extension of the Velvet assembler to a de novo metagenomic assembler utilizing supervised learning (2015)
  • Author(s): Afiahayati, Sato, K., and Sakakibara, Y.
  • Journal Title: DNA Research Volume: 22 Issue: 1 Pages: 69-77
  • DOI: 10.1093/dnares/dsu041
  • Peer Reviewed / Open Access / Acknowledgement Compliant
• [Journal Article] Whole genome complete resequencing of Bacillus subtilis natto by combining long reads with high-quality short reads (2014)
  • Author(s): Kamada, M., Hase, S., Sato, K., Toyoda, A., Fujiyama, A., Sakakibara, Y.
  • Journal Title: PLOS ONE Volume: 9 Issue: 10 Pages: e109999-e109999
  • DOI: 10.1371/journal.pone.0109999
  • Peer Reviewed / Open Access / Acknowledgement Compliant
• [Presentation] Rtools: a web server for various secondary structural analyses on single RNA sequences (2016)
  • Author(s): Hamada, M., Ono, Y., Kiryu, H., Sato, K., Kato, Y., Fukunaga, T., Mori, R., Asai, K.
  • Organizer: The 21st Annual meeting of the RNA Society (RNA2016)
  • Place of Presentation: 京都国際会館（京都府・京都市）
  • Year and Date: 2016-06-28
  • Int'l Joint Research
• [Presentation] Accurate prediction of RNA-RNA interactions from sequence data incorporating interaction site accessibility (2016)
  • Author(s): Kato, Y., Mori, T., Sato, K., Maegawa, S., Hosokawa, H., Akutsu, T.
  • Organizer: The 21st Annual meeting of the RNA Society (RNA2016)
  • Place of Presentation: 京都国際会館（京都府・京都市）
  • Year and Date: 2016-06-28
  • Int'l Joint Research
• [Presentation] 統計的検定結果に基づく高精度クラスタリングアルゴリズムの開発 (2015)
  • Author(s): 青戸良賢，八谷剛史，奥村和弘， 長谷純崇，佐藤健吾，若林雄一，榊原康文
  • Organizer: 情報処理学会第43回バイオ情報学研究会
  • Place of Presentation: 慶應義塾大学（神奈川県横浜市）
  • Year and Date: 2015-09-12
• [Presentation] 双対分解によるマルチプルアラインメント (2015)
  • Author(s): 穴水拓郎，榊原康文，佐藤健吾
  • Organizer: 情報処理学会第43回バイオ情報学研究会
  • Place of Presentation: 慶應義塾大学（神奈川県横浜市）
  • Year and Date: 2015-09-12
• [Presentation] A max-margin model for predicting residue-base contacts in protein-RNA interactions (2015)
  • Author(s): Sato, K., Kashiwagi, S., Sakakibara, Y.
  • Organizer: GIW/InCoB 2015
  • Place of Presentation: 科学未来館（東京都江東区）
  • Year and Date: 2015-09-09
  • Int'l Joint Research
• [Presentation] Prediction of gene structures from RNA-seq data using dual decomposition (2015)
  • Author(s): Inatsuki, T, Sato, K., Sakakibara, Y.
  • Organizer: 情報処理学会第42回バイオ情報学研究会
  • Place of Presentation: 沖縄先端科学技術大学院大学（沖縄県恩納村）
  • Year and Date: 2015-06-02
• [Presentation] 機械学習を用いたタンパク質とRNAのコンタクト予測 (2014)
  • Author(s): 佐藤健吾，柏木駿也，榊原康文
  • Organizer: 第3回生命医薬情報学連合大会，日本バイオインフォマティクス学会2014年年会
  • Place of Presentation: 仙台国際センター（宮城県・仙台市）
  • Year and Date: 2014-10-02 – 2014-10-04
• [Presentation] 機械学習を用いたタンパク質とRNAのコンタクト予測 (2014)
  • Author(s): 佐藤健吾，柏木駿也，榊原康文
  • Organizer: 第16回日本RNA学会年会
  • Place of Presentation: ウィンクあいち（愛知県・名古屋市）
  • Year and Date: 2014-07-23 – 2014-07-25
• [Presentation] 機械学習を用いたマススペクトルデータからの糖鎖構造推定法の開発 (2013)
  • Author(s): 雲崎翔太郎
  • Organizer: 情報処理学会第34回バイオ情報学研究会
  • Place of Presentation: 沖縄科学技術大学院大学
• [Presentation] A machine learning based approach to de novo sequencing of glycans from mass spectrometry data (2013)
  • Author(s): Shotaro Kumozaki
  • Organizer: 日本バイオインフォマティクス学会 2013年年会
  • Place of Presentation: タワーホール船堀