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

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.

[1]  Wenliang Du,et al.  Secure and private sequence comparisons , 2003, WPES '03.

[2]  Bart Preneel,et al.  Advances in cryptology - EUROCRYPT 2000 : International Conference on the Theory and Application of Cryptographic Techniques, Bruges, Belgium, May 14-18, 2000 : proceedings , 2000 .

[3]  Zvi Galil,et al.  Proceedings of the 30th IEEE symposium on Foundations of computer science , 1994, FOCS 1994.

[4]  Andrew Chi-Chih Yao,et al.  Protocols for secure computations , 1982, FOCS 1982.

[5]  Joe Kilian,et al.  One-Round Secure Computation and Secure Autonomous Mobile Agents , 2000, ICALP.

[6]  Donald Beaver.  Minimal-Latency Secure Function Evaluation , 2000, EUROCRYPT.

[7]  Silvio Micali,et al.  How to play ANY mental game , 1987, STOC.

[8]  A. Yao,et al.  Fair exchange with a semi-trusted third party (extended abstract) , 1997, CCS '97.

[9]  Moni Naor,et al.  Efficient oblivious transfer protocols , 2001, SODA '01.

[10]  Vitaly Shmatikov,et al.  Towards Practical Privacy for Genomic Computation , 2008, 2008 IEEE Symposium on Security and Privacy (sp 2008).

[11]  Silvio Micali,et al.  Computationally Private Information Retrieval with Polylogarithmic Communication , 1999, EUROCRYPT.

[12]  Stefan Katzenbeisser,et al.  Privacy preserving error resilient dna searching through oblivious automata , 2007, CCS '07.

[13]  Robin Milner,et al.  On Observing Nondeterminism and Concurrency , 1980, ICALP.

[14]  Pascal Paillier,et al.  Public-Key Cryptosystems Based on Composite Degree Residuosity Classes , 1999, EUROCRYPT.

[15]  Eyal Kushilevitz,et al.  Private information retrieval , 1998, JACM.

[16]  Benny Pinkas,et al.  Fairplay - Secure Two-Party Computation System , 2004, USENIX Security Symposium.

[17]  Yuval Ishai,et al.  Selective private function evaluation with applications to private statistics , 2001, PODC '01.

[18]  Yehuda Lindell,et al.  A Proof of Yao's Protocol for Secure Two-Party Computation , 2004, Electron. Colloquium Comput. Complex..

[19]  Jacques Stern,et al.  Advances in Cryptology — EUROCRYPT ’99 , 1999, Lecture Notes in Computer Science.

[20]  Deni Elliott,et al.  Genetic Information Nondiscrimination Act , 2008 .

[21]  Ran Canetti,et al.  Security and Composition of Multiparty Cryptographic Protocols , 2000, Journal of Cryptology.

[22]  Moti Yung,et al.  Non-interactive cryptocomputing for NC/sup 1/ , 1999, 40th Annual Symposium on Foundations of Computer Science (Cat. No.99CB37039).

[23]  Rafail Ostrovsky,et al.  Replication is not needed: single database, computationally-private information retrieval , 1997, Proceedings 38th Annual Symposium on Foundations of Computer Science.