Finding missing patterns

Shunsuke Inenaga, Teemu Kivioja, Veli Mäkinen

研究成果: ジャーナルへの寄稿記事

6 引用 (Scopus)

抄録

Consider the following problem: Find the shortest pattern that does not occur in a given text. To make the problem non-trivial, the pattern is required to consist only of characters that occur in the text. This problem can be solved easily in linear time using the suffix tree of the text. In this paper, we study an extension of this problem, namely the missing patterns problem: Find the shortest pair of patterns that do not occur close to each other in a given text, i.e., the distance between their occurrences is always greater than a given threshold a. We show that the missing patterns problem can be solved in O(min(αn log n, n2)) time, where n is the size of the text. For the special case where both pairs are required to have the same length, we give an algorithm with time complexity O(αn log log n). The problem is motivated by optimization of multiplexed nested-PCR.

元の言語英語
ページ(範囲)463-474
ページ数12
ジャーナルLecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)
3240
出版物ステータス出版済み - 12 1 2004
外部発表Yes

Fingerprint

Suffix Tree
Time Complexity
Linear Time
Text
Optimization
Character

All Science Journal Classification (ASJC) codes

  • Theoretical Computer Science
  • Computer Science(all)

これを引用

Finding missing patterns. / Inenaga, Shunsuke; Kivioja, Teemu; Mäkinen, Veli.

:: Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics), 巻 3240, 01.12.2004, p. 463-474.

研究成果: ジャーナルへの寄稿記事

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