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 1
イベント23rd International Symposium on String Processing and Information Retrieval, SPIRE 2016 - Beppu, Japan
継続期間: 2016 10 182016 10 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
CountryJapan
CityBeppu
Period16/10/1816/10/20

ASJC Scopus subject areas

  • Theoretical Computer Science
  • Computer Science(all)

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