Fast genome-wide detection of RNA genes using coarse-grained structural information

• Project/Area Number: 15K00401
• 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: Osaka University (2016-2017); Kyoto University (2015)
• Principal Investigator: KATO Yuki 大阪大学, 医学系研究科, 助教 (10511280)
• Project Period (FY): 2015-04-01 – 2018-03-31
• Project Status: Completed (Fiscal Year 2017)
• Budget Amount: ¥4,420,000 (Direct Cost: ¥3,400,000、Indirect Cost: ¥1,020,000); Fiscal Year 2017: ¥1,430,000 (Direct Cost: ¥1,100,000、Indirect Cost: ¥330,000); Fiscal Year 2016: ¥1,560,000 (Direct Cost: ¥1,200,000、Indirect Cost: ¥360,000); Fiscal Year 2015: ¥1,430,000 (Direct Cost: ¥1,100,000、Indirect Cost: ¥330,000)
• Keywords: RNA / 遺伝子発見 / ２次構造 / ゲノムワイド / ノンコーディングRNA / 比較ゲノム / ゲノムワイド配列比較

Outline of Final Research Achievements

For the purpose of incomplete genomic annotation of non-coding RNAs, here we presented a computational method for detecting structured RNA genes that two organisms share in common in their genomic sequences, which aims to compare their coarse-grained structures. Computational experiments with both simulated and authentic chromosomal data indicate that the proposed method achieves high sensitivity for the detection of structured RNA genes. We conclude that our approach can be useful as a comparative genomic pre-screening of structured RNAs.

Research Products

• [Int'l Joint Research] コペンハーゲン大学(デンマーク)
• [Int'l Joint Research] コペンハーゲン大学(デンマーク)
• [Int'l Joint Research] コペンハーゲン大学(デンマーク)
• [Journal Article] Alignment-free comparative genomic screen for structured RNAs using coarse-grained secondary structure dot plots (2017)
  • Author(s): Yuki Kato, Jan Gorodkin and Jakob Hull Havgaard
  • Journal Title: BMC Genomics Volume: 18 Issue: 1 Pages: 935-935
  • DOI: 10.1186/s12864-017-4309-y
  • Peer Reviewed / Open Access / Int'l Joint Research
• [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
• [Presentation] スペクトラルグラフ理論を応用した１細胞RNA-seqデータのトップダウン型クラスタリング (2018)
  • Author(s): 蒲原 純, 加藤 有己, 河原 行郎
  • Organizer: 第53回情報処理学会バイオ情報学研究会
• [Presentation] ビット列のソートに基づくリード直接比較による高速省メモリゲノム構造変異解析 (2018)
  • Author(s): 新村 啓介, 加藤 有己, 河原 行郎
  • Organizer: 第53回情報処理学会バイオ情報学研究会
• [Presentation] Fast and efficient alignment-free comparative genomic screen for structured RNAs with DotcodeR (2017)
  • Author(s): Yuki Kato, Jan Gorodkin and Jakob Hull Havgaard
  • Organizer: The 25th Conference on Intelligent Systems for Molecular Biology and the 16th European Conference on Computational Biology (ISMB/ECCB2017)
  • Int'l Joint Research
• [Presentation] Accurate prediction of RNA-RNA interactions from sequence data incorporating interaction site accessibility (2016)
  • Author(s): Yuki Kato, Tomoya Mori, Kengo Sato, Shingo Maegawa, Hiroshi Hosokawa and Tatsuya Akutsu
  • Organizer: The 2016 joint annual meeting of the RNA Society and the RNA Society of Japan (RNA2016)
  • Place of Presentation: 国立京都国際会館（京都市左京区）
  • Year and Date: 2016-06-28
  • Int'l Joint Research
• [Presentation] Rtools: a web server for various secondary structural analyses on single RNA sequences (2016)
  • Author(s): Michiaki Hamada, Yukiteru Ono, Hisanori Kiryu, Kengo Sato, Yuki Kato, Tsukasa Fukunaga, Ryota Mori and Kiyoshi Asai
  • Organizer: The 2016 joint annual meeting of the RNA Society and the RNA Society of Japan (RNA2016)
  • Place of Presentation: 国立京都国際会館（京都市左京区）
  • Year and Date: 2016-06-28
  • Int'l Joint Research
• [Presentation] A computational method for dissecting single-cell populations based on transcriptomic data (2016)
  • Author(s): Yuki Kato and Wataru Fujibuchi
  • Organizer: CiRA/ISSCR 2016 International Symposium
  • Place of Presentation: 京都大学百周年時計台記念館（京都市左京区）
  • Year and Date: 2016-03-22
  • Int'l Joint Research
• [Presentation] Genomic screen for structured RNAs using coarse-grained dot plots (2015)
  • Author(s): Yuki Kato, Jakob Hull Havgaard and Jan Gorodkin
  • Organizer: 生命医薬情報学連合大会2015年大会
  • Place of Presentation: 京都大学おうばくプラザ（京都府宇治市）
  • Year and Date: 2015-10-29
• [Presentation] Development of a pipeline for analysis of meta- and single-cell genomic sequences (2015)
  • Author(s): Kenta Kobayashi, Midori Yuji, Yuki Kato, Takeaki Taniguchi, Toru Maruyama, Michihiro Ito, Susumu Goto, Haruko Takeyama and Wataru Fujibuchi
  • Organizer: 生命医薬情報学連合大会2015年大会
  • Place of Presentation: 京都大学おうばくプラザ（京都府宇治市）
  • Year and Date: 2015-10-29
• [Presentation] Genomic screen for structured RNAs using coarse-grained dot plots (2015)
  • Author(s): Yuki Kato, Jakob Hull Havgaard and Jan Gorodkin
  • Organizer: The First Joint Conference between GIW and InCoB (GIW/InCoB2015)
  • Place of Presentation: 未来館（東京都江東区）
  • Year and Date: 2015-09-09
  • Int'l Joint Research
• [Presentation] De novo prediction of structured RNAs from genomes using coarse-grained dot plots (2015)
  • Author(s): Yuki Kato
  • Organizer: Computational Analysis of RNA Structure and Function
  • Place of Presentation: ベナスケ（スペイン）
  • Year and Date: 2015-07-19
  • Int'l Joint Research