A linear-time algorithm for the 1-mismatch problem

Nikola Stojanovic, Piotr Berman, Deborah Gumucio, Ross Hardison, Webb Miller

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

34 Scopus citations

Abstract

For sequence alignments (which can be viewed simply as rectangular arrays of characters), a frequent need is to identify regions, each consisting of a run of consecutive columns, that have some particular property. The 1-mismatch problem is to locate all maximal regions in a given alignment for which there exists a (not necessarily unique) “center” sequence such that inside the region alignment rows are within Hamming distance 1 from the center. We first describe some properties of these regions and their centers, and then use these properties to construct an algorithm that for a dxn alignment runs in time θ(nd) and extra space θ(d) (beyond that needed for the storage of the alignment itself).

Original languageEnglish (US)
Title of host publicationAlgorithms and Data Structures - 5th International Workshop, WADS 1997, Proceedings
EditorsFrank Dehne, Jorg-Rudiger Sack, Andrew Rau-Chaplin, Roberto Tamassia
PublisherSpringer Verlag
Pages126-135
Number of pages10
ISBN (Print)3540633073, 9783540633075
DOIs
StatePublished - 1997
Event5th International Workshop on Algorithms and Data Structures, WADS 1997 - Halifax, Canada
Duration: Aug 6 1997Aug 8 1997

Publication series

NameLecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)
Volume1272
ISSN (Print)0302-9743
ISSN (Electronic)1611-3349

Other

Other5th International Workshop on Algorithms and Data Structures, WADS 1997
CountryCanada
CityHalifax
Period8/6/978/8/97

All Science Journal Classification (ASJC) codes

  • Theoretical Computer Science
  • Computer Science(all)

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