A linear-space algorithm for the substring constrained alignment problem

    研究成果: Conference contribution

    抄録

    In a string similarity metric adopting affine gap penalties, we propose a quadratic-time, linear-space algorithm for the following constrained string alignment problem. The input of the problem is a pair of strings to be aligned and a pattern given as a string. Let an occurrence of the pattern in a string be a minimal substring of the string that is most similar to the pattern. Then, the output of the problem is a highestscoring alignment of the pair of strings that matches an occurrence of the pattern in one string and an occurrence of the pattern in the other, where the score of the alignment excludes the similarity between the matched occurrences of the pattern. This problem may arise when we know that each of the strings has exactly one meaningful occurrence of the pattern and want to determine a putative pair of such occurrences based on homology of the strings.

    本文言語English
    ホスト出版物のタイトルString Processing and Information Retrieval - 23rd International Symposium, SPIRE 2016, Proceedings
    編集者Shunsuke Inenaga, Kunihiko Sadakane, Tetsuya Sakai
    出版社Springer-Verlag
    ページ15-21
    ページ数7
    ISBN(印刷版)9783319460482
    DOI
    出版ステータスPublished - 2016 1月 1
    イベント23rd International Symposium on String Processing and Information Retrieval, SPIRE 2016 - Beppu, Japan
    継続期間: 2016 10月 182016 10月 20

    出版物シリーズ

    名前Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)
    9954 LNCS
    ISSN(印刷版)0302-9743
    ISSN(電子版)1611-3349

    Other

    Other23rd International Symposium on String Processing and Information Retrieval, SPIRE 2016
    国/地域Japan
    CityBeppu
    Period16/10/1816/10/20

    ASJC Scopus subject areas

    • 理論的コンピュータサイエンス
    • コンピュータ サイエンス(全般)

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