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A Linear-Space Algorithm for the Substring Constrained Alignment Problem

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String Processing and Information Retrieval (SPIRE 2016)

Part of the book series: Lecture Notes in Computer Science ((LNTCS,volume 9954))

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Abstract

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 highest-scoring 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.

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Author information

Authors and Affiliations

  1. Graduate School of Agricultural Science, Tohoku University, 1-1, Amamiyamachi, Tsutsumidori, Aobaku, Sendai, 981-8555, Japan

    Yoshifumi Sakai

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  1. Yoshifumi Sakai
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Correspondence to Yoshifumi Sakai .

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Editors and Affiliations

  1. Kyushu University , Fukuoka, Japan

    Shunsuke Inenaga

  2. Mathematical Informatics, University of Tokyo , Tokyo, Japan

    Kunihiko Sadakane

  3. Computer Science, Waseda University , Tokyo, Japan

    Tetsuya Sakai

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Sakai, Y. (2016). A Linear-Space Algorithm for the Substring Constrained Alignment Problem. In: Inenaga, S., Sadakane, K., Sakai, T. (eds) String Processing and Information Retrieval. SPIRE 2016. Lecture Notes in Computer Science(), vol 9954. Springer, Cham. https://doi.org/10.1007/978-3-319-46049-9_2

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  • DOI: https://doi.org/10.1007/978-3-319-46049-9_2

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  • Publisher Name: Springer, Cham

  • Print ISBN: 978-3-319-46048-2

  • Online ISBN: 978-3-319-46049-9

  • eBook Packages: Computer ScienceComputer Science (R0)

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