Fast identification of approximately matching substrings

  • Archie L. Cobbs
Conference paper
Part of the Lecture Notes in Computer Science book series (LNCS, volume 807)


Let two strings S, T over a finite alphabet Σ be given, and let M be an arbitrary relation on Σ×Σ. Define an approximate match (x,y) of two length m subwords (substrings) xS, yT when M(x i ,y i , for all 1≤im. A match implies all the local alignments (without insertions and deletions) which are pairings of specific occurrances of x and y. A match (x,y) is maximal if there exists no longer match (u, v) such that all of the local alignments implied by (x,y) are contained in a local alignment implied by (u,v). We give an efficient algorithm for finding all maximal matches between S and T. The algorithm runs in time bounded by the sum of the lengths of the maximal matches, at worst. OΣ¦2n2). The main application is identifying homologous regions of protein sequences.


Linear Time Local Alignment Maximal Match Suffix Tree Finite Alphabet 
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Copyright information

© Springer-Verlag Berlin Heidelberg 1994

Authors and Affiliations

  • Archie L. Cobbs
    • 1
  1. 1.Computer Science DivisionUniversity of California BerkeleyBerkeley

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