Practical Private DNA String Searching and Matching through Efficient Oblivious Automata Evaluation

  • Authors:
  • Keith B. Frikken

  • Affiliations:
  • Department of Computer Science and Systems Analysis, Miami University, Oxford, 45056

  • Venue:
  • Proceedings of the 23rd Annual IFIP WG 11.3 Working Conference on Data and Applications Security XXIII
  • Year:
  • 2009

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Abstract

In [18] it was shown that the ability to perform oblivious automata evaluation was useful for performing DNA searching and matching. By oblivious automata evaluation we mean that one participant has a finite state machine and the other participant has a sequence, and at the end of the protocol the sequence owner learns whether the machine accepts the sequence. A protocol was given in [18], but it required O (n ) rounds (where n is the number of characters in the sequence) and O (mn ) modular exponentiations (where m is the number of states in the automata). Both of these factors limit the applicability of this approach. In this paper we propose a new protocol that requires only O (1) rounds and reduces the number of modular exponentiations to O (n ) without revealing any additional information. We have implemented both schemes and have shown experimentally that our scheme is two to three orders of magnitude faster than the previous scheme.