Algorithms for solving the sum-of-ratios problem using polynomialrelaxations and its application to sequence alignment

2008 Fiscal Year Final Research Report

• Project/Area Number: 19510135
• Research Category: Grant-in-Aid for Scientific Research (C)
• Allocation Type: Single-year Grants
• Section: 一般
• Research Field: Social systems engineering/Safety system
• Research Institution: Muroran Institute of Technology
• Principal Investigator: SHI Jianming Muroran Institute of Technology, 工学部, 准教授 (70287465)
• Project Period (FY): 2007 – 2008
• Keywords: 最適化 / 分数和情報学計画 / 生体情報学

Research Abstract

生体生命における情報の中に共通配列(モチーフ)を探し出すことを研究の目的である. モチーフを評価するため, 情報量に基き, ある種の分数和を最大化することが必要である. 本研究はこのような既存の分数和を最大にする計算方法(アルゴリズム)を研究し, 2005に発表されたモチーフ抽出アルゴリズムを大幅改良した. 数値実験の結果では,計算速度を2900倍に速くすることに成功した.

Research Products

• [Journal Article] A Modified Algorithm for Sequence Alignment Using Ant Colony System (2009)
  • Author(s): Ai Mikami, Jianming Shi
  • Journal Title: IPSJ Transactions on Bioinformatics Vol 2 Pages: 63-73
  • Peer Reviewed
• [Presentation] Solving Sum of Linear Ratios Problem using Linear Relaxation (2008)
  • Author(s): J. Shi
  • Place of Presentation: Hilton University of Florida, Gainesville, FL
  • Year and Date: 20080128-30
• [Presentation] A new algorithm for solving the sum-of-linear-ratio problem (2007)
  • Author(s): J.Shi
  • Organizer: ICOTA7
  • Place of Presentation: International Convention Center, Kobe
  • Year and Date: 20071216-20
• [Presentation] INFORS 2007 (2007)
  • Author(s): J. Shi
  • Organizer: Washington State Convention & Trade Center
  • Place of Presentation: Washington State Convention & Trade Center, Seattle, WA
  • Year and Date: 2007-04-07
• [Remarks]
  • URL: http://www.mmm.muroran-it.ac.jp/~shi/