Sequencing by Hybridization in Few Rounds

Research output: Chapter in Book/Report/Conference proceedingChapterpeer-review

1 Scopus citations


Sequencing by Hybridization (SBH) is a method for reconstructing an unknown DNA string based on substring queries: Using hybridization experiments, one can determine for each string in a given set of strings, whether the string appears in the target string, and use this information to reconstruct the target string. We study the problem when the queries are performed in rounds, where the queries in each round depend on the answers to the queries in the previous rounds. We give an algorithm that can reconstruct almost all strings of length n using 2 rounds with O(n logα n/logα log α n) queries per round, and an algorithm that uses log α* n - Ω(1) rounds with O(n) queries per round, where a is the size of the alphabet. We also consider a variant of the problem in which for each substring query, the answer is whether the string appears once in the target, appears at least twice in the target, or does not appear in the target. For this problem, we give an algorithm that uses 3 rounds of O(n) queries. In all our algorithms, the lengths of the query strings are Θ(logα n). Our results improve the previous results of Margaritis and Skiena [17] and Frieze and Halldórsson [10].

Original languageEnglish
Title of host publicationAlgorithms - ESA 2003
Subtitle of host publication11th Annual European Symposium, Budapest, Hungary, September 16-19, 2003. Proceedings
EditorsGiuseppe di Battista, Uri Zwick
PublisherSpringer Verlag
Number of pages11
ISBN (Print)3540200649, 9783540200642
StatePublished - 1 Jan 2003
Externally publishedYes
Event11th Annual European Symposium on Algorithms - Budapest, Hungary
Duration: 16 Sep 200319 Sep 2003

Publication series

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


Conference11th Annual European Symposium on Algorithms
Abbreviated titleESA 2003

ASJC Scopus subject areas

  • Theoretical Computer Science
  • General Computer Science


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