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An Easy Automata Based Algorithm for Testing Coding Properties of Infinite Sets of (DNA) Words

  • Michelangelo Cianciulli
  • Rocco Zaccagnino
  • Rosalba Zizza
Conference paper
Part of the Lecture Notes in Computer Science book series (LNCS, volume 7505)

Abstract

Recently a new interest towards the design of efficient algorithms for testing whether a language X is a code, has arisen from (wet) DNA Computing. Indeed, in this context, the final computation is a concatenation of DNA strands (words) that must satisfy some restrictions (DNA properties) to prevent them from interacting in undesirable ways. Efficient algorithms (and implementations) have been designed when X is a finite set. In this paper we provide an algorithm (and a Java implementation) for testing whether an infinite but regular set of words is a code that avoids some unwanted cross hybridizations. The algorithm runs in O(n 2), where n is the sum of the numbers of states and transitions in a finite state automaton recognizing X.

Keywords

DNA codeword design problem DNA Computing Codes Finite State Automata 

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Copyright information

© Springer-Verlag Berlin Heidelberg 2012

Authors and Affiliations

  • Michelangelo Cianciulli
    • 1
  • Rocco Zaccagnino
    • 1
  • Rosalba Zizza
    • 1
  1. 1.Dipartimento di InformaticaUniversità di SalernoFiscianoItaly

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