Identifying periodic occurrences of a template with applications to protein structure

Vincent A. Fischetti, Gad M. Landau, Jeanette P. Schmidt, Peter H. Sellers

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


We consider a string matching problem where the pattern is a template that matches many different strings with various degrees of perfection. The quality of a match is given by a penalty matrix that assigns each pair of characters a score that characterizes how well the characters match. Superfluous characters in the text and superfluous characters in the pattern may also occur and the respective penalties for such gaps in the alignment are also given by the penalty matrix. For a text T of length n, and a template P of length m, we wish to find the best alignment of T with Pn, which is the concatenation of n copies of P, (m will typically be much smaller than n). Such an alignment can simply be obtained by solving a dynamic programming problem of size O(n2m), and ignoring the periodic character of Pn. We show that the structure of Pn can be exploited and the problem reduced to essentially solving a dynamic programming of size O(mn). If the complexity of computing gap penalties is O(1), (which is frequently the case), our algorithm runs in O(mn) time. The problem was motivated by a protein structure problem.

Original languageEnglish
Title of host publicationCombinatorial Pattern Matching - 3rd Annual Symposium, Proceedings
EditorsAlberto Apostolico, Maxime Crochemore, Zvi Galil, Zvi Galil, Udi Manber
PublisherSpringer Verlag
Number of pages10
ISBN (Print)9783540560241
StatePublished - 1992
Externally publishedYes
Event3rd Annual Symposium on Combinatorial Pattern Matching, 1992 - Tucson, United States
Duration: 29 Apr 19921 May 1992

Publication series

NameLecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)
Volume644 LNCS
ISSN (Print)0302-9743
ISSN (Electronic)1611-3349


Conference3rd Annual Symposium on Combinatorial Pattern Matching, 1992
Country/TerritoryUnited States

Bibliographical note

Publisher Copyright:
© Springer-Verlag Berlin Heidelberg 1992.

ASJC Scopus subject areas

  • Theoretical Computer Science
  • General Computer Science


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