Abstract
NGS (next-generation sequencing) is bringing the need to efficiently handle large volumes of patient data, maintaining privacy laws, such as those with secure protocols that ensure patients DNA confidentiality. Although there are multiple file representations for genomic data, the FASTA format is perhaps the most used and popular. As far as we know, FASTA encryption is being addressed with general purpose encryption methods, without exploring a compact representation. In this paper, we propose Cryfa, a new fast encryption method to store securely FASTA files in a compact form. The main differences between a general encryption approach and Cryfa are the reduction of storage, up to approximately three times, without compromising security, and the possibility of integration with pipelines. The core of the encryption method uses a symmetric approach, the AES (Advanced Encryption Standard). Cryfa implementation is freely available, under license GPLv3, at https://github.com/pratas/cryfa.
This is a preview of subscription content, log in via an institution to check access.
Access this chapter
Tax calculation will be finalised at checkout
Purchases are for personal use only
References
Mardis, E.R.: The impact of next-generation sequencing technology on genetics. Trends Genet. 24(3), 133–141 (2008)
Schlosberg, A.: Data security in genomics: a review of australian privacy requirements and their relation to cryptography in data storage. J. Pathol. Inform. 7, 6 (2016)
Mohammed, M.H., Dutta, A., Bose, T., Chadaram, S., Mande, S.S.: DELIMINATE - a fast and efficient method for loss-less compression of genomic sequences. Bioinformatics 28(19), 2527–2529 (2012)
Bose, T., Mohammed, M.H., Dutta, A., Mande, S.S.: BIND-an algorithm for loss-less compression of nucleotide sequence data. J. Biosci. 37(4), 785–789 (2012)
Pinho, A.J., Pratas, D.: MFCompress: a compression tool for fasta and multi-fasta data. Bioinformatics 30, 117–118 (2013)
Benoit, G., Lemaitre, C., Lavenier, D., Drezen, E., Dayris, T., Uricaru, R., Rizk, G.: Reference-free compression of high throughput sequencing data with a probabilistic de bruijn graph. BMC Bioinformatics 16(1), 288 (2015)
Kim, M., Zhang, X., Ligo, J.G., Farnoud, F., Veeravalli, V.V., Milenkovic, O.: MetaCRAM: an integrated pipeline for metagenomic taxonomy identification and compression. BMC Bioinformatics 17(1), 94 (2016)
Cao, M.D., Dix, T.I., Allison, L., Mears, C.: A simple statistical algorithm for biological sequence compression. In: Proceedings of the Data Compression Conference, DCC-2007, Snowbird, Utah, pp. 43–52, March 2007
Pratas, D., Pinho, A.J., Ferreira, P.: Efficient compression of genomic sequences. In: Proceedings of the Data Compression Conference, DCC-2016, Snowbird, Utah, pp. 231–240, March 2016
Hosseini, M., Pratas, D., Pinho, A.J.: A survey on data compression methods for biological sequences. Information 7(4), 56 (2016)
Daemen, J., Rijmen, V.: AES proposal: Rijndael. EC (1999)
Biryukov, A., Khovratovich, D., Nikolić, I.: Distinguisher and related-key attack on the full AES-256. In: Halevi, S. (ed.) CRYPTO 2009. LNCS, vol. 5677, pp. 231–249. Springer, Heidelberg (2009). doi:10.1007/978-3-642-03356-8_14
Ashokkumar, C., Giri, R.P., Menezes, B.: Highly efficient algorithms for AES key retrieval in cache access attacks. In: IEEE European Symposium on Security and Privacy (EuroS&P), 261–275. IEEE (2016)
Gullasch, D., Bangerter, E., Krenn, S.: Cache games-bringing access-based cache attacks on AES to practice. In: IEEE Symposium on Security and Privacy, pp. 490–505. IEEE (2011)
Keerthi, V.K., et al.: Taxonomy of SSL/TLS attacks. Int. J. Comput. Netw. Inf. Secur. 8(2), 15 (2016)
Meyer, C., Schwenk, J.: Lessons learned from previous SSL/TLS attacks-a brief chronology of attacks and weaknesses. IACR Cryptology ePrint Archive 2013, 49 (2013)
Church, D., Deanna, M., Schneider, V., et al.: Modernizing reference genome assemblies. PLoS Biol. 9(7), e1001091 (2011)
Bouillaguet, C., Derbez, P., Dunkelman, O., Fouque, P.A., Keller, N., Rijmen, V.: Low-data complexity attacks on aes. IEEE Trans. Inf. Theory 58(11), 7002–7017 (2012)
Acknowledgments
This work was partially funded by FEDER (Programa Operacional Factores de Competitividade - COMPETE) and by National Funds through the FCT - Foundation for Science and Technology, in the context of the projects UID/CEC/00127/2013, PTCD/EEI-SII/6608/2014.
Author information
Authors and Affiliations
Corresponding author
Editor information
Editors and Affiliations
Rights and permissions
Copyright information
© 2017 Springer International Publishing AG
About this paper
Cite this paper
Pratas, D., Hosseini, M., Pinho, A.J. (2017). Cryfa: A Tool to Compact and Encrypt FASTA Files. In: Fdez-Riverola, F., Mohamad, M., Rocha, M., De Paz, J., Pinto, T. (eds) 11th International Conference on Practical Applications of Computational Biology & Bioinformatics. PACBB 2017. Advances in Intelligent Systems and Computing, vol 616. Springer, Cham. https://doi.org/10.1007/978-3-319-60816-7_37
Download citation
DOI: https://doi.org/10.1007/978-3-319-60816-7_37
Published:
Publisher Name: Springer, Cham
Print ISBN: 978-3-319-60815-0
Online ISBN: 978-3-319-60816-7
eBook Packages: EngineeringEngineering (R0)