RNA interactome prediction in eukaryotic genomes

• Project/Area Number: 22700304
• Research Category: Grant-in-Aid for Young Scientists (B)
• Allocation Type: Single-year Grants
• Research Field: Bioinformatics/Life informatics
• Research Institution: Hirosaki University
• Principal Investigator: TANEDA Akito 弘前大学, 大学院・理工学研究科, 准教授 (70332492)
• Project Period (FY): 2010 – 2011
• Project Status: Completed (Fiscal Year 2011)
• Budget Amount: ¥2,210,000 (Direct Cost: ¥1,700,000、Indirect Cost: ¥510,000); Fiscal Year 2011: ¥910,000 (Direct Cost: ¥700,000、Indirect Cost: ¥210,000); Fiscal Year 2010: ¥1,300,000 (Direct Cost: ¥1,000,000、Indirect Cost: ¥300,000)
• Keywords: 生体生命情報学 / RNA工学 / ゲノム / 遺伝子 / RNA

Research Abstract

We have developed computational RNA sequence analysis tools including a prediction system for RNA sequence alignment and an RNA sequence design method on the basis of multi-objective genetic algorithm. Alignments and secondary structures predicted by our system can give useful information for RNA-RNA interaction prediction. Moreover, our RNA sequence design method can be applied to RNA device design problems which are difficult for the other previous RNA sequence design methods.

Research Products

• [Journal Article] Multi-objective genetic algorithm for pseudoknotted RNA sequence design (2012)
  • Author(s): Akito Taneda
  • Journal Title: Frontiers in Genetics Volume: 3巻 Pages: 36-36
  • Peer Reviewed
• [Journal Article] MODENA : a multi-objective RNA inverse folding (2011)
  • Author(s): Akito Taneda
  • Journal Title: Advances and Applications in Bioinformatics and Chemistry Volume: 4巻 Pages: 1-12
  • Peer Reviewed
• [Journal Article] A Web Server for Multi-objective Pairwise RNA Sequence Alignment with an Index for Selecting Accurate Alignments (2011)
  • Author(s): Akito Taneda
  • Journal Title: IPSJ Transactions on Bioinformatics Volume: 4巻 Pages: 2-8
  • NAID: 130000770573
  • Peer Reviewed
• [Presentation] Computational RNA sequence design toward creation of artificial functional RNAs (2011)
  • Author(s): 種田晃人
  • Organizer: 第34回日本分子生物学会年会(シンポジウム講演)
  • Place of Presentation: パシフィコ横浜(神奈川県)
  • Year and Date: 2011-12-14
• [Presentation] Computational RNA sequence design toward creation of artificial functional RNAs (2011)
  • Author(s): 種田晃人
  • Organizer: 第34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)(シンポジウム講演)
  • Year and Date: 2011-12-14
• [Presentation] 構造変化を伴う機能性RNAの配列設計 (2011)
  • Author(s): 種田晃人
  • Organizer: 第10回RNA/RNPを見つける会
  • Place of Presentation: カルチャーリゾートフェストーネ(沖縄県)
  • Year and Date: 2011-09-16
• [Presentation] RNAの逆フォールディング (2011)
  • Author(s): 種田晃人
  • Organizer: 次世代バイオインフォマティクス研究会2011
  • Place of Presentation: 産業技術総合研究所北海道センター(北海道)
  • Year and Date: 2011-08-02
• [Presentation] 多目的最適化によるRNA配列解析 (2010)
  • Author(s): 種田晃人
  • Organizer: 新しい RNA/RNPを見つける会2010
  • Place of Presentation: 弘前大学コラボレーションセター(青森県)
  • Year and Date: 2010-09-06
• [Presentation] 多目的最適化によるRNA配列解析 (2010)
  • Author(s): 種田晃人
  • Organizer: 新しいRNA/RNPを見つける会2010
  • Place of Presentation: 弘前大学コラボレーションセンター(青森県)
  • Year and Date: 2010-09-06
• [Presentation] A multi-objective evolutionary algorithm for RNA sequence design (2010)
  • Author(s): 種田晃人
  • Organizer: 生命情報工学研究センターワークショップ2010(CBRC2010)
  • Place of Presentation: 産業技術総合研究所臨海副都心センター別館(東京都)
  • Year and Date: 2010-07-27
• [Presentation] A MULTI-OBJECTIVE EVOLUTIONARY ALGORITHM FOR RNA SEQUENCE DESIGN (2010)
  • Author(s): 種田晃人
  • Organizer: 生命情報工学研究センターワークショップ2010(CBRC2010)
  • Place of Presentation: 産業技術総合研究所 臨海副都心センター別館(東京都)
  • Year and Date: 2010-07-27
• [Remarks]
  • URL: http://rna.eit.hirosaki-u.ac.jp/cofolga2mo/srv/
• [Remarks]
  • URL: http://rna.eit.hirosaki-u.ac.jp/modena/
• [Remarks]
  • URL: http://rna.eit.hirosaki-u.ac.jp/modena/
• [Remarks]
  • URL: http://rna.eit.hirosaki-u.ac.jp/cofolga2mo/srv/