A linear-space algorithm for the substring constrained alignment problem

Research output: Chapter in Book/Report/Conference proceedingConference contribution

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 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.

Original languageEnglish
Title of host publicationString Processing and Information Retrieval - 23rd International Symposium, SPIRE 2016, Proceedings
EditorsShunsuke Inenaga, Kunihiko Sadakane, Tetsuya Sakai
PublisherSpringer-Verlag
Pages15-21
Number of pages7
ISBN (Print)9783319460482
DOIs
Publication statusPublished - 2016 Jan 1
Event23rd International Symposium on String Processing and Information Retrieval, SPIRE 2016 - Beppu, Japan
Duration: 2016 Oct 182016 Oct 20

Publication series

NameLecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)
Volume9954 LNCS
ISSN (Print)0302-9743
ISSN (Electronic)1611-3349

Other

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

ASJC Scopus subject areas

  • Theoretical Computer Science
  • Computer Science(all)

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  • Cite this

    Sakai, Y. (2016). A linear-space algorithm for the substring constrained alignment problem. In S. Inenaga, K. Sadakane, & T. Sakai (Eds.), String Processing and Information Retrieval - 23rd International Symposium, SPIRE 2016, Proceedings (pp. 15-21). (Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics); Vol. 9954 LNCS). Springer-Verlag. https://doi.org/10.1007/978-3-319-46049-9_2