On the shared substring alignment problem

Gad M. Landau, Michal Ziv-Ukelson

Research output: Contribution to conferencePaperpeer-review


A new problem in sequence comparison, given a set of strings S1, S2 ... Sc and a target string T Si = BiY Fi is introduced. Y is the subsequence common to all of strings Si. The goal is to compute similarity of all strings Si with T, without computing the part of Y again and again. How to reduce the O(nl) runtime work for the common subsequence Y in each string to O(n), at the cost of only O(n2+nl) work at preprocessing time, where n is target size and l is the size of Y.

Original languageEnglish
Number of pages11
StatePublished - 2000
Externally publishedYes
Event11th Annual ACM-SIAM Symposium on Discrete Algorithms - San Francisco, CA, USA
Duration: 9 Jan 200011 Jan 2000


Conference11th Annual ACM-SIAM Symposium on Discrete Algorithms
CitySan Francisco, CA, USA

ASJC Scopus subject areas

  • Software
  • General Mathematics


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