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A study on preprocessing for time-efficiently aligning sequences

Research Project

Project/Area Number 22500001
Research Category

Grant-in-Aid for Scientific Research (C)

Allocation TypeSingle-year Grants
Section一般
Research Field Fundamental theory of informatics
Research InstitutionTohoku University

Principal Investigator

SAKAI Yoshifumi  東北大学, 大学院・農学研究科, 准教授 (10277361)

Project Period (FY) 2010 – 2012
Project Status Completed (Fiscal Year 2012)
Budget Amount *help
¥2,210,000 (Direct Cost: ¥1,700,000、Indirect Cost: ¥510,000)
Fiscal Year 2012: ¥910,000 (Direct Cost: ¥700,000、Indirect Cost: ¥210,000)
Fiscal Year 2011: ¥650,000 (Direct Cost: ¥500,000、Indirect Cost: ¥150,000)
Fiscal Year 2010: ¥650,000 (Direct Cost: ¥500,000、Indirect Cost: ¥150,000)
Keywordsアルゴリズム理論 / 文字列比較 / アルゴリズム
Research Abstract

Problems of finding a ‘good' alignment of two strings have many applications in computing the similarity between strings. This study proposed algorithms for some of such problems. By exploiting information obtained from preprocessing, these algorithms can perform faster than the previous algorithms. The problems for which the algorithms were proposed include the problem in which only one of two strings is allowed to be preprocessed because of an one-line environment, and the problem in which strings to be aligned are compressed in a certain manner.

Report

(4 results)
  • 2012 Annual Research Report   Final Research Report ( PDF )
  • 2011 Annual Research Report
  • 2010 Annual Research Report
  • Research Products

    (21 results)

All 2013 2012 2011 2010

All Journal Article (8 results) (of which Peer Reviewed: 8 results) Presentation (13 results)

  • [Journal Article] Computing the longest common subsequences of two run-length encoded strings3L.-M. Chao, T.-s. Hsu, and D.-T. Lee (Eds.)2012

    • Author(s)
      Yoshifumi Sakai
    • Journal Title

      ISAAC 2012, LNCS

      Volume: 7676 Pages: 197-206

    • DOI

      10.1007/978-3-642-35261-4_23

    • ISBN
      9783642352607, 9783642352614
    • Related Report
      2012 Final Research Report
    • Peer Reviewed
  • [Journal Article] A Fast On-Line Algorithm for the Longest Common Subsequence Problem with Constant Alphabet2012

    • Author(s)
      Yoshifumi Sakai
    • Journal Title

      IEICE Transactions on Fundamentals of Electronics, Communications and Computer Sciences

      Volume: E95-A Issue: 1 Pages: 354-361

    • DOI

      10.1587/transfun.E95.A.354

    • NAID

      10030535198

    • ISSN
      0916-8508, 1745-1337
    • Related Report
      2012 Final Research Report 2011 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Computing the longest common subsequence of two run-length encoded strings2012

    • Author(s)
      Yoshifumi Sakai
    • Journal Title

      Lecture Notes in Computer Science, Algorithms and Computation

      Volume: 7676 Pages: 197-206

    • Related Report
      2012 Annual Research Report
    • Peer Reviewed
  • [Journal Article] A new algorithm for the characteristic string problem under loose similarity criteria, T. Asano et al. (Eds.)2011

    • Author(s)
      Yoshifumi Sakai
    • Journal Title

      ISAAC 2011, LNCS

      Volume: 7074 Pages: 663-672

    • DOI

      10.1007/978-3-642-25591-5_68

    • ISBN
      9783642255908, 9783642255915
    • Related Report
      2012 Final Research Report
    • Peer Reviewed
  • [Journal Article] A first algorithm for multiplying min-sum permutation2011

    • Author(s)
      Yoshifumi Sakai
    • Journal Title

      Discrete Applied Mathematics

      Volume: 159 Issue: 17 Pages: 2175-2183

    • DOI

      10.1016/j.dam.2011.06.022

    • Related Report
      2011 Annual Research Report
    • Peer Reviewed
  • [Journal Article] A new algorithm for the characteristic string problem under loose similarity criteria2011

    • Author(s)
      Yoshifumi Sakai
    • Journal Title

      Lecture Notes in Computer Science

      Volume: 7074 Pages: 663-672

    • Related Report
      2011 Annual Research Report
    • Peer Reviewed
  • [Journal Article] An almost quadratic time algorithm for sparse spliced alignment2011

    • Author(s)
      Yoshifumi Sakai
    • Journal Title

      Theory of Computing Systems

      Volume: 48 Pages: 189-210

    • Related Report
      2010 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Flexible computation of the longest common subsequence of run-length encoded strings2010

    • Author(s)
      Yoshifumi Sakai
    • Journal Title

      The 13^<th> Japan-Korea Joint Workshop on Algorithms and Computation

      Pages: 72-79

    • Related Report
      2010 Annual Research Report
    • Peer Reviewed
  • [Presentation] 部分文字列最大密度索引2013

    • Author(s)
      酒井義文
    • Organizer
      2012年度冬のLAシンポジウム
    • Place of Presentation
      京都市・京都大学
    • Related Report
      2012 Final Research Report
  • [Presentation] 部分文字列最大密度索引2013

    • Author(s)
      酒井義文
    • Organizer
      2012年度冬のLAシンポジウム
    • Place of Presentation
      京都府京都市京都大学
    • Related Report
      2012 Annual Research Report
  • [Presentation] 海藻全単射の漸減構築2012

    • Author(s)
      酒井義文
    • Organizer
      2011年度冬のLAシンポジウム
    • Place of Presentation
      京都
    • Year and Date
      2012-01-31
    • Related Report
      2011 Annual Research Report
  • [Presentation] run長符号化文字列の最強共通部分列計算2012

    • Author(s)
      酒井義文
    • Organizer
      2012年度夏のLAシンポジウム
    • Place of Presentation
      宮津市・宮津ロイヤルホテル
    • Related Report
      2012 Final Research Report
  • [Presentation] 海藻全単射の漸減構築2012

    • Author(s)
      酒井義文
    • Organizer
      2011年度冬のLAシンポジウム
    • Place of Presentation
      京都市・京都大学
    • Related Report
      2012 Final Research Report
  • [Presentation] run長符号化文字列の最長共通部分列計算2012

    • Author(s)
      酒井義文
    • Organizer
      2012年度夏のLAシンポジウム
    • Place of Presentation
      京都府宮津市宮津ロイヤルホテル
    • Related Report
      2012 Annual Research Report
  • [Presentation] 緩い類似性判定基準のもとでの特徴文字列問題アルゴリズム2011

    • Author(s)
      酒井義文
    • Organizer
      2011年度夏のLAシンポジウム
    • Place of Presentation
      湖西
    • Year and Date
      2011-07-20
    • Related Report
      2011 Annual Research Report
  • [Presentation] 最長共通部分配列計算におけるrun長の対数時間寄与2011

    • Author(s)
      酒井義文
    • Organizer
      2010年冬のLAシンポジウム
    • Place of Presentation
      京都
    • Year and Date
      2011-02-02
    • Related Report
      2010 Annual Research Report
  • [Presentation] 緩い類似税判定基準のもとでの特徴文字列問題アルゴリズム2011

    • Author(s)
      酒井義文
    • Organizer
      2011年度夏のLAシンポジウム
    • Place of Presentation
      湖西市・ザヴィラ浜名湖
    • Related Report
      2012 Final Research Report
  • [Presentation] 最長共通部分も配列計算におけるrun長の対数時間寄与2011

    • Author(s)
      酒井義文
    • Organizer
      2010年度冬のLAシンポジウム
    • Place of Presentation
      京都市・京都大学
    • Related Report
      2012 Final Research Report
  • [Presentation] 可能な最長部分パターンの文字列照合問題2010

    • Author(s)
      酒井義文
    • Organizer
      2010年夏のLaシンポジウム
    • Place of Presentation
      氷見
    • Year and Date
      2010-07-21
    • Related Report
      2010 Annual Research Report
  • [Presentation] Flexible computation of the longest common subsequence of run-length encoded strings2010

    • Author(s)
      Yoshifumi Sakai
    • Organizer
      The 13th Japan-Korea Joint Workshop on Algorithms and Computation
    • Place of Presentation
      金沢市・金沢市文化ホール
    • Related Report
      2012 Final Research Report
  • [Presentation] 可能な最長部分パターンの文字列照合問題2010

    • Author(s)
      酒井義文
    • Organizer
      2010年度夏のLAシンポジウム
    • Place of Presentation
      氷見市・九殿浜温泉ひみのはな
    • Related Report
      2012 Final Research Report

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Published: 2010-08-23   Modified: 2019-07-29  

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