Calculation of Characteristics of Constraints for DNA Sequences and its Applications to Code Construction

• Project/Area Number: 21560394
• Research Category: Grant-in-Aid for Scientific Research (C)
• Allocation Type: Single-year Grants
• Section: 一般
• Research Field: Communication/Network engineering
• Research Institution: Gifu University
• Principal Investigator: KAMABE Hiroshi 岐阜大学, 工学部, 教授 (80169614)
• Project Period (FY): 2009 – 2011
• Project Status: Completed (Fiscal Year 2011)
• Budget Amount: ¥2,860,000 (Direct Cost: ¥2,200,000、Indirect Cost: ¥660,000); Fiscal Year 2011: ¥650,000 (Direct Cost: ¥500,000、Indirect Cost: ¥150,000); Fiscal Year 2010: ¥1,040,000 (Direct Cost: ¥800,000、Indirect Cost: ¥240,000); Fiscal Year 2009: ¥1,170,000 (Direct Cost: ¥900,000、Indirect Cost: ¥270,000)
• Keywords: 情報理論 / 通信路容量 / 計算論的言語理論 / DNAコンピュータ / DNA計算 / 符号理論 / 入力制約のある通信路 / 記号力学系 / 制約符号 / 入力制約 / コンマフリー符号 / whiplashモデル / 文脈自由文法

Research Abstract

In this research we have investigated the calculation of the capacity of constraints for DNA computation and coding scheme for the constraints. We have obtained two kinds of results. One of them is how to calculate the capacity of constraint described as context free grammar. The second is how to calculate the capacity of constraints for parsing DNA programs uqiquely. From the last result we have obtained a guideline for constructing codes for the constraints.

Research Products

• [Journal Article] Outfix-free and intercode con-straints for DNA squences (2011)
  • Author(s): H. Kamabe
  • Journal Title: Proceeding of 2011 IEEE International Symposium on Information Theory Pages: 1574-1578
  • Peer Reviewed
• [Journal Article] Outfix-free and intercode constraints for DNA sequences (2011)
  • Author(s): Hiroshi Kamabe
  • Journal Title: Proceeding of 2011, IEEE International Symposium on Information Theory Pages: 622-627
  • DOI: 10.1109/isit.2011.6033809
  • Peer Reviewed
• [Journal Article] Outfix-free and Intercode Constraints for DNA Sequences (2011)
  • Author(s): Hiroshi Kamabe
  • Journal Title: Proceedings of the International Symposium on Information Thoery 2011 Volume: (採録決定,未発刊)
  • Peer Reviewed
• [Journal Article] Constraints for DNA sequences by formal languages and its capacity (2010)
  • Author(s): H. Kamabe
  • Journal Title: Proceeding of Nature and Biologically Inspired Computing 2010 Pages: 622-627
  • Peer Reviewed
• [Journal Article] Constraints for DNA Sequences by Formal Language and its Capacity (2010)
  • Author(s): Hiroshi Kamabe
  • Journal Title: Proceedings of the World Congress on Nature and Biologically Inspired Computing 2010 Pages: 629-634
  • Peer Reviewed
• [Presentation] On constraints for DNA sequences (2011)
  • Author(s): Hiroshi Kamabe
  • Organizer: 2011 Information Theory and its Applications Workshop
  • Place of Presentation: カリフォルニア大学サンディエゴ校
  • Year and Date: 2011-02-11
• [Presentation] Outfix-free and intercode con-straints for DNA squences (2011)
  • Author(s): H. Kamabe
  • Organizer: 2011 IEEE Interna-tional Symposium on Information Theory
  • Place of Presentation: Saint Petersberg
• [Presentation] Constraints for DNA Sequences by Formal Language and its Capacity (2010)
  • Author(s): Hiroshi Kamabe
  • Organizer: The 32rd Symposium on Information Theory and its Application (SITA2010)
  • Place of Presentation: 信州松代ロイヤルホテル
  • Year and Date: 2010-12-01
• [Presentation] DNA系列の制約について (2010)
  • Author(s): 鎌部浩
  • Organizer: 電子情報通信学会情報理論研究会技術研究報告
  • Place of Presentation: 東北学院大学
  • Year and Date: 2010-09-22
• [Presentation] DNA系列の制約について (2010)
  • Author(s): 鎌部浩
  • Organizer: 電子情報通信学会 情報理論研究会
  • Place of Presentation: 東北学院大学
  • Year and Date: 2010-09-22
• [Presentation] Constraints for DNA sequences by formal languages and its capacity (2010)
  • Author(s): H. Kamabe
  • Organizer: Nature and Biologically Inspired Computing 2010
  • Place of Presentation: Ki-takyushu
• [Presentation] Constraints for DNA sequences by formal languages and its capacity (2010)
  • Author(s): H. Kamabe
  • Organizer: 情報理論とその応用シンポジウム
  • Place of Presentation: 信州