Article

Secure outsourcing of DNA searching via finite automata

Authors:

Marina Blanton and

Mehrdad AliasgariAuthors Info & Claims

DBSec'10: Proceedings of the 24th annual IFIP WG 11.3 working conference on Data and applications security and privacy

June 2010

Pages 49 - 64

Published: 21 June 2010 Publication History

Abstract

This work treats the problem of error-resilient DNA searching via oblivious evaluation of finite automata, where a client has a DNA sequence, and a service provider has a pattern that corresponds to a genetic test. Error-resilient searching is achieved by representing the pattern as a finite automaton and evaluating it on the DNA sequence, where privacy of both the pattern and the DNA sequence must be preserved. Interactive solutions to this problem already exist, but can be a burden on the participants. Thus, we propose techniques for secure outsourcing of finite automata evaluation to computational servers, which do not learn any information. Our techniques are applicable to any type of finite automata, but the optimizations are tailored to DNA searching.

References

[1]

Atallah, M., Kerschbaum, F., Du, W.: Secure and private sequence comparisons. In: WPES, pp. 39-44 (2003).

Digital Library

[2]

Jha, S., Kruger, L., Shmatikov, V.: Towards practical privacy for genomic computation. In: IEEE Symposium on Security and Privacy, pp. 216-230 (2008).

Digital Library

[3]

Troncoso-Pastoriza, J., Katzenbeisser, S., Celik, M.: Privacy preserving error resilient DNA searching through oblivious automata. In: ACM CCS, pp. 519-528 (2007).

Digital Library

[4]

Frikken, K.: Practical private DNA string searching and matching through efficient oblivious automata evaluation. In: DBSec, pp. 81-94 (2009).

Digital Library

[5]

Bruekers, F., Katzenbeisser, S., Kursawe, K., Tuyls, P.: Privacy-preserving matching of DNA profiles. ePrint Cryptology Archive Report 2008/203 (2008).

[6]

Wang, R., Wang, X., Li, Z., Tang, H., Reiter, M., Dong, Z.: Privacy-preserving genomic computation through program specialization. In: ACM CCS, pp. 338-347 (2009).

Digital Library

[7]

Atallah, M., Li, J.: Secure outsourcing of sequence comparisons. In: PET, pp. 63-78 (2004).

Digital Library

[8]

Atallah, M., Li, J.: Secure outsourcing of sequence comparisons. International Journal of Information Security 4(4), 277-287 (2005).

Digital Library

[9]

Genetic Testing for Health, Disease & Ancestry; DNA Test - 23andMe, http://www.23andme.com

[10]

Blanton, M., Aliasgari, M.: Secure outsourcing of DNA searching via finite automata. Technical Report 2010-03, University of Notre Dame (2010).

[11]

Szajda, D., Pohl, M., Owen, J., Lawson, B.: Toward a practical data privacy scheme for a distributed implementation of the Smith-Waterman genome sequence comparison algorithm. In: NDSS (2006).

[12]

Kantarcioglu, M., Jiang, W., Liu, Y., Malin, B.: A cryptographic approach to securely share and query genomic sequences. IEEE Transactions on Information Technology in Biomedicine 12(5), 606-617 (2008).

Digital Library

[13]

Franklin, M., Gondree, M., Mohassel, P.: Communication-efficient private protocols for longest common subsequence. In: RSA, pp. 265-278 (2009).

Digital Library

[14]

Gondree, M., Mohassel, P.: Longest common subsequence as private search. In: WPES, pp. 81-90 (2009).

Digital Library

[15]

Naor, M., Pinkas, B.: Efficient oblivious transfer protocols. In: SODA, pp. 448-457 (2001).

Digital Library

[16]

Lipmaa, H.: An oblivious transfer protocol with log-squared communication. In: Zhou, J., López, J., Deng, R.H., Bao, F. (eds.) ISC 2005. LNCS, vol. 3650, pp. 314-328. Springer, Heidelberg (2005).

Digital Library

[17]

Gentry, C., Ramzan, Z.: Single-database private information retrieval with constant communication rate. In: ICALP, pp. 803-815 (2005).

Digital Library

[18]

Naor, M., Pinkas, B.: Oblivious transfer and polynomial evaluation. In: STOC (1999).

Digital Library

[19]

Crescenzo, G., Malkin, T., Ostrovsky, R.: Single database private information retrieval implies oblivious transfer. In: Preneel, B. (ed.) EUROCRYPT 2000. LNCS, vol. 1807, pp. 122-138. Springer, Heidelberg (2000).

Digital Library

[20]

Cachin, C., Micali, S., Stadler, M.: Computationally private information retrieval with polylogarithmic communication. In: Stern, J. (ed.) EUROCRYPT 1999. LNCS, vol. 1592, pp. 402-414. Springer, Heidelberg (1999).

Digital Library

[21]

Kushilevitz, E., Ostrovsky, R.: Replication is not needed: Single database, computationally-private information retrieval. In: IEEE FOCS, pp. 364-373 (1997).

Digital Library

[22]

Melchor, C.A., Deswarte, Y.: Single-database private information retrieval schemes: Overview, performance study, and usage with statistical databases. In: Privacy in Statistical Databases, pp. 257-265 (2006).

Digital Library

[23]

Aguilar-Melchor, C., Gaborit, P.: A lattice-based computationally-efficient private information retrieval protocol. In: WEWORC (2007).

[24]

Damgard, I., Jurik, M.: A length-flexible threshold cryptosystem with applications. In: Australasian Conference on Information Security and Privacy (2007).

Digital Library

[25]

Bae, H.: Design and analysis for log-squared and log private information retrieval (2008).

[26]

Melchor, C., Crespin, B., Gaborit, P., Jolivet, V.: High-speed private information retrieval computation on GPU. In: IEEE SECURWARE (2008).

Digital Library

[27]

Goldreich, O., Micali, S., Wigderson, A.: How to play any mental game. In: STOC, pp. 218-229 (1987).

Digital Library

[28]

Canetti, R.: Security and composition of multiparty cryptographic protocols. Journal of Cryptology 13(1), 143-202 (2000).

Digital Library

Cited By

Sudo HJimbo MNuida KShimizu K(2019)Secure Wavelet MatrixIEEE/ACM Transactions on Computational Biology and Bioinformatics10.1109/TCBB.2018.281403916:5(1675-1684)Online publication date: 1-Sep-2019
https://dl.acm.org/doi/10.1109/TCBB.2018.2814039
Samadani MBerenjkoob MBlanton M(2019)Secure pattern matching based on bit parallelismInternational Journal of Information Security10.1007/s10207-018-0410-818:3(371-391)Online publication date: 1-Jun-2019
https://dl.acm.org/doi/10.1007/s10207-018-0410-8
Shan ZRen KBlanton MWang C(2018)Practical Secure Computation OutsourcingACM Computing Surveys10.1145/315836351:2(1-40)Online publication date: 20-Feb-2018
https://dl.acm.org/doi/10.1145/3158363
Show More Cited By

Index Terms

Secure outsourcing of DNA searching via finite automata
1. Information systems
  1. Data management systems
    1. Data structures
      1. Data layout
        Data encryption
2. Security and privacy
  1. Cryptography

Index terms have been assigned to the content through auto-classification.

Recommendations

Privacy preserving error resilient dna searching through oblivious automata
CCS '07: Proceedings of the 14th ACM conference on Computer and communications security

Human Desoxyribo-Nucleic Acid (DNA) sequences offer a wealth of information that reveal, among others, predisposition to various diseases and paternity relations. The breadth and personalized nature of this information highlights the need for privacy-...
Read More
Oblivious two-way finite automata: Decidability and complexity

We investigate the descriptional complexity and decidability of obliviousness for two-way finite automata. In particular, we consider the simulation of two-way deterministic finite automata (2DFAs) by oblivious 2DFAs, the simulation of oblivious 2DFAs ...
Read More
An autonomous DNA model for finite state automata

In this paper we introduce an autonomous DNA model for finite state automata. This model called sticker automaton model is based on the hybridisation of single stranded DNA molecules (stickers) encoding transition rules and input data. The computation ...
Read More

Comments

Information & Contributors

Information

Published In

cover image Guide Proceedings

DBSec'10: Proceedings of the 24th annual IFIP WG 11.3 working conference on Data and applications security and privacy

June 2010

375 pages

ISBN:3642137385

Editors:
Sara Foresti
DTI, Universitò degli Studi di Milano, Crema, CR, Italy
,
Sushil Jajodia
CSIS, George Mason University, Fairfax, VA

Publisher

Springer-Verlag

Berlin, Heidelberg

Publication History

Published: 21 June 2010

Qualifiers

Article

Contributors

Other Metrics

View Article Metrics

Bibliometrics & Citations

Bibliometrics

Article Metrics

20
Total Citations
View Citations
0
Total Downloads

Downloads (Last 12 months)0
Downloads (Last 6 weeks)0

Other Metrics

View Author Metrics

Citations

Cited By

Sudo HJimbo MNuida KShimizu K(2019)Secure Wavelet MatrixIEEE/ACM Transactions on Computational Biology and Bioinformatics10.1109/TCBB.2018.281403916:5(1675-1684)Online publication date: 1-Sep-2019
https://dl.acm.org/doi/10.1109/TCBB.2018.2814039
Samadani MBerenjkoob MBlanton M(2019)Secure pattern matching based on bit parallelismInternational Journal of Information Security10.1007/s10207-018-0410-818:3(371-391)Online publication date: 1-Jun-2019
https://dl.acm.org/doi/10.1007/s10207-018-0410-8
Shan ZRen KBlanton MWang C(2018)Practical Secure Computation OutsourcingACM Computing Surveys10.1145/315836351:2(1-40)Online publication date: 20-Feb-2018
https://dl.acm.org/doi/10.1145/3158363
Humbert MAyday EHubaux JTelenti A(2017)Quantifying Interdependent Risks in Genomic PrivacyACM Transactions on Privacy and Security10.1145/303553820:1(1-31)Online publication date: 6-Feb-2017
https://dl.acm.org/doi/10.1145/3035538
Zhou KAfifi MRen J(2017)ExpSOS: Secure and Verifiable Outsourcing of Exponentiation Operations for Mobile Cloud ComputingIEEE Transactions on Information Forensics and Security10.1109/TIFS.2017.271094112:11(2518-2531)Online publication date: 1-Nov-2017
https://dl.acm.org/doi/10.1109/TIFS.2017.2710941
Ayday EHubaux JWeippl EKatzenbeisser SKruegel CMyers AHalevi S(2016)Privacy and Security in the Genomic EraProceedings of the 2016 ACM SIGSAC Conference on Computer and Communications Security10.1145/2976749.2976751(1863-1865)Online publication date: 24-Oct-2016
https://dl.acm.org/doi/10.1145/2976749.2976751
Chen XSusilo WLi JWong DMa JTang STang Q(2015)Efficient algorithms for secure outsourcing of bilinear pairingsTheoretical Computer Science10.1016/j.tcs.2014.09.038562:C(112-121)Online publication date: 11-Jan-2015
https://dl.acm.org/doi/10.1016/j.tcs.2014.09.038
Akgün MBayrak AOzer BSağıroğlu M(2015)Privacy preserving processing of genomic dataJournal of Biomedical Informatics10.1016/j.jbi.2015.05.02256:C(103-111)Online publication date: 1-Aug-2015
https://dl.acm.org/doi/10.1016/j.jbi.2015.05.022
Wei LReiter M(2015)Toward practical encrypted email that supports private, regular-expression searchesInternational Journal of Information Security10.1007/s10207-014-0268-314:5(397-416)Online publication date: 1-Oct-2015
https://dl.acm.org/doi/10.1007/s10207-014-0268-3
Karvelas NPeter AKatzenbeisser STews EHamacher KAhn GDatta A(2014)Privacy-Preserving Whole Genome Sequence Processing through Proxy-Aided ORAMProceedings of the 13th Workshop on Privacy in the Electronic Society10.1145/2665943.2665962(1-10)Online publication date: 3-Nov-2014
https://dl.acm.org/doi/10.1145/2665943.2665962
Show More Cited By

View Options

View options

Get Access

Login options

Check if you have access through your login credentials or your institution to get full access on this article.

Full Access

Get this Publication

Media

Figures

Other

Tables

View Table of Contents