An easy automata based algorithm for testing coding properties of infinite sets of (DNA) words

  • Authors:

  • Michelangelo Cianciulli;Rocco Zaccagnino;Rosalba Zizza

  • Affiliations:

  • Dipartimento di Informatica, Università di Salerno, Fisciano, SA, Italy;Dipartimento di Informatica, Università di Salerno, Fisciano, SA, Italy;Dipartimento di Informatica, Università di Salerno, Fisciano, SA, Italy

  • Venue:
  • TPNC'12 Proceedings of the First international conference on Theory and Practice of Natural Computing
  • Year:
  • 2012

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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(n2), where n is the sum of the numbers of states and transitions in a finite state automaton recognizing X.