Finding missing patterns

Shunsuke Inenaga, Teemu Kivioja, Veli Mäkinen

Research output: Contribution to journalArticle

6 Citations (Scopus)

Abstract

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.

Original languageEnglish
Pages (from-to)463-474
Number of pages12
JournalLecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)
Volume3240
Publication statusPublished - Dec 1 2004
Externally publishedYes

All Science Journal Classification (ASJC) codes

  • Theoretical Computer Science
  • Computer Science(all)

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