Restricting SBH ambiguity via restriction enzymes

Steven Skiena, Sagi Snir

Research output: Chapter in Book/Report/Conference proceedingConference contributionpeer-review


The expected number of n-base long sequences consistent with a given SBH spectrum grows exponentially with n, which severely limits the potential range of applicability of SBH even in an error-free setting. Restriction enzymes (RE) recognize specific patterns and cut the DNA molecule at all locations of that pattern. The output of a restriction assay is the set of lengths of the resulting fragments. By augmenting the SBH spectrum with the target string’s RE spectrum, we can eliminate much of the ambiguity of SBH. In this paper, we build on [20] to enhance the resolving power of restriction enzymes. We give a hardness result for the SBH+RE problem, and supply improved heuristics for the existing backtracking algorithm. We prove a lower bound on the number restriction enzymes required for unique reconstruction, and show experimental results that are not far from this bound.

Original languageEnglish
Title of host publicationAlgorithms in Bioinformatics - 2nd International Workshop,WABI 2002, Proceedings
EditorsRoderic Guigo, Dan Gusfield
PublisherSpringer Verlag
Number of pages14
ISBN (Print)3540442111, 9783540442110
StatePublished - 2002
Externally publishedYes
Event2nd International Workshop on Algorithms in Bioinformatics, WABI 2002 - Rome, Italy
Duration: 17 Sep 200221 Sep 2002

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


Conference2nd International Workshop on Algorithms in Bioinformatics, WABI 2002

Bibliographical note

Publisher Copyright:
© Springer-Verlag Berlin Heidelberg 2002.

ASJC Scopus subject areas

  • Theoretical Computer Science
  • Computer Science (all)


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