English  |  正體中文  |  简体中文  |  Items with full text/Total items : 54367/62174 (87%)
Visitors : 14086621      Online Users : 63
RC Version 6.0 © Powered By DSPACE, MIT. Enhanced by NTHU Library IR team.
Scope Tips:
  • please add "double quotation mark" for query phrases to get precise results
  • please goto advance search for comprehansive author search
  • Adv. Search
    HomeLoginUploadHelpAboutAdminister Goto mobile version
    National Tsing Hua University Institutional Repository > 電機資訊學院 > 資訊工程學系 > 會議論文  >  Efficient algorithms for regular expression constrained sequence alignment


    Please use this identifier to cite or link to this item: http://nthur.lib.nthu.edu.tw/dspace/handle/987654321/66324


    Title: Efficient algorithms for regular expression constrained sequence alignment
    Authors: Chung, Yun-Sheng;Lu, Chin Lung;Tang, Chuan Yi
    教師: 唐傳義
    Date: 2006
    Publisher: Springer Verlag
    Relation: Lecture Notes in Computer Science,Volume 4009,2006,頁 389-400
    Keywords: Pattern matching
    Algorithms
    Database systems
    Computational complexity
    Problem solving
    Proteins
    Constraint theory
    Abstract: Imposing constraints is an effective means to incorporate biological knowledge into alignment procedures. As in the PROSITE database, functional sites of proteins can be effectively described as regular expressions. In an alignment of protein sequences it is natural to expect that functional motifs should be aligned together. Due to this motivation, in CPM 2005 Arslan introduced the regular expression constrained sequence alignment problem and proposed an algorithm which can take time and space up to O(| summation |2 | V|4n2) and O(| summation |2 |V|4n), respectively, where summation is the alphabet, n is the sequence length, and V is the set of states in an automaton equivalent to the input regular expression. In this paper we propose a more efficient algorithm solving this problem which takes O(|V|3n2) time and O(|V|2n) space in the worst case. If |V| = O(log n) we propose another algorithm with time complexity O(|V|2 log |V| n2). The time complexity of our algorithms is independent of summation , which is desirable in protein applications where the formulation of this problem originates; a factor of | summation |2 = 400 in the time complexity of the previously proposed algorithm would significantly affect the efficiency in practice.
    URI: http://www.springerlink.com/
    http://nthur.lib.nthu.edu.tw/dspace/handle/987654321/66324
    Appears in Collections:[資訊工程學系] 會議論文

    Files in This Item:

    File Description SizeFormat
    index.html0KbHTML222View/Open


    在NTHUR中所有的資料項目都受到原著作權保護,僅提供學術研究及教育使用,敬請尊重著作權人之權益。若須利用於商業或營利,請先取得著作權人授權。
    若發現本網站收錄之內容有侵害著作權人權益之情事,請權利人通知本網站管理者(smluo@lib.nthu.edu.tw),管理者將立即採取移除該內容等補救措施。

    SFX Query

    與系統管理員聯絡

    DSpace Software Copyright © 2002-2004  MIT &  Hewlett-Packard  /   Enhanced by   NTU Library IR team Copyright ©   - Feedback