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Context-Dependent String Matching

In: Sequences

Author

Listed:
  • Alan A. Bertossi

    (Università di Pisa, Dipartimento di Informatica)

  • Elena Lodi

    (Università di Pisa, Dipartimento di Informatica)

  • Fabrizio Luccio

    (Università di Pisa, Dipartimento di Informatica)

  • Linda Pagli

    (Università di Salerno, Dipartimento di Informatica e Applicazioni)

Abstract

The approximate string matching problem consists of finding all the occurrences of a pattern P of length m in a text T of length n, m≪n, where at most k differences are allowed between P and each of its occurrences in T. Various types of differences have been studied in the literature. We introduce here the concept of context-dependent errors, where the differences between P and T depend on errors in T that are functions of the context of P and/or T, and develop sequential and parallel algorithms for some relevant sets of weighted errors. In particular, we allow: context-dependent mismatches, extra and missing characters (Problem I); the same errors plus transpositions of two consecutive characters (Problem II); and a more general choice of errors (Problem III). A set of theoretical results allows to solve Problems I and II with O(kn) time sequential algorithms, and O(k + log m) parallel time on a PRAM model with max{n+k+l, m2{ processors. Problem III is instead solved in O(mn) sequential time, and O(m+log n) parallel time with n+1 processors on a feasible bounded degree network.

Suggested Citation

  • Alan A. Bertossi & Elena Lodi & Fabrizio Luccio & Linda Pagli, 1990. "Context-Dependent String Matching," Springer Books, in: Renato M. Capocelli (ed.), Sequences, pages 25-40, Springer.
    • Handle: RePEc:spr:sprchp:978-1-4612-3352-7_2
    DOI: 10.1007/978-1-4612-3352-7_2
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