APM  Vol.3 No.7 A , October 2013
Variant Map System to Simulate Complex Properties of DNA Interactions Using Binary Sequences
ABSTRACT

Stream cipher, DNA cryptography and DNA analysis are the most important R&D fields in both Cryptography and Bioinformatics. HC-256 is an emerged scheme as the new generation of stream ciphers for advanced network security. From a random sequencing viewpoint, both sequences of HC-256 and real DNA data may have intrinsic pseudo-random properties respectively. In a recent decade, many DNA sequencing projects are developed on cells, plants and animals over the world into huge DNA databases. Researchers notice that mammalian genomes encode thousands of large noncoding RNAs (lncRNAs), interact with chromatin regulatory complexes, and are thought to play a role in localizing these complexes to target loci across the genome. It is a challenge target using higher dimensional visualization tools to organize various complex interactive properties as visual maps. The Variant Map System (VMS) as an emerging scheme is systematically proposed in this paper to apply multiple maps that used four Meta symbols as same as DNA or RNA representations. System architecture of key components and core mechanism on the VMS are described. Key modules, equations and their I/O parameters are discussed. Applying the VM System, two sets of real DNA sequences from both sample human (noncoding DNA) and corn (coding DNA) genomes are collected in comparison with pseudo DNA sequences generated by HC-256 to show their intrinsic properties in higher levels of similar relationships among relevant DNA sequences on 2D maps. Sample 2D maps are listed and their characteristics are illustrated under controllable environment. Visual results are briefly analyzed to explore their intrinsic properties on selected genome sequences.


Cite this paper
J. Zheng, W. Zhang, J. Luo, W. Zhou and R. Shen, "Variant Map System to Simulate Complex Properties of DNA Interactions Using Binary Sequences," Advances in Pure Mathematics, Vol. 3 No. 7, 2013, pp. 5-24. doi: 10.4236/apm.2013.37A002.
References
[1]   ESTREAM Project.
http://en.wikipedia.org/wiki/ESTREAM

[2]   H. J. Wu, “Stream Cipher HC-256,” 2004.
http://www.ecrypt.eu.org/stream/p3ciphers/hc/hc256_p3.pdf

[3]   M. Santha and U. V. Vazirani, “Generating Quasi-Random Sequences from Slightly Random Sources,” Journal of Computer and System Sciences, Vol. 33, No. 1, 1986, pp. 75-87.
http://dx.doi.org/10.1016/0022-0000(86)90044-9

[4]   P. Goutam and M. Subhamoy, “RC4 Stream Cipher and Its Variants,” CRC Press, Boca Raton, 2012.

[5]   M. Gude, “Concept for a High-Performance Random Number Generator Based on Physical Random Noise,” Frequenz, Vol. 39, No. 7-8, 1985, pp. 187-190.

[6]   D. Eastlake, S. D. Crocker and J. I. Schiller, “Randomness Requirements for Security, RFC 1750,” 1994.

[7]   C. Plumb, “Truly Random Numbers,” Dr. Dobbs Journal, Vol. 19, No. 13, 1994, pp. 113-115.

[8]   G. B. Agnew, “Random Source for Cryptographic Systems,” Springer-Verlag, Berlin, 1988, pp. 77-81.

[9]   A. Gehani, T. LaBean and J. Reif, “DNA-Based Cryptography,” DIMACS Series in Discrete Mathematica and Theoretical Computer Science, Vol. 54, 2000, pp. 233-249.
http://www.cs.duke.edu/~reif/paper/DNAcrypt/DNA5.DNAcrypt.pdf

[10]   B. E. Bernstein, E. Birney, I. Dunham, et al., “An Integrated Encyclopedia of DNA Elements in the Human Genome,” Nature, Vol. 489, No. 7414, 2012, pp. 57-74.
http://dx.doi.org/10.1038/nature11247

[11]   E. Pennisi, “Genomics. ENCODE Project Writes Eulogy for Junk DNA,” Science, Vol. 337, No. 6099, 2012, pp. 1159-1161. http://dx.doi.org/10.1126/science.337.6099.1159

[12]   M. Schooniger and A. von Haeseler, “Simulating Efficiently the Evolution of DNA Sequences,” Computer Applications in the Biosciences, Vol. 11, No. 1, 1995, pp. 111-115.

[13]   F. Piva and G. Principato, “RANDNA: A Random DNA Sequence Generator,” Silico Biology, Vol. 6, No. 3, 2006, pp. 253-258.

[14]   C. M. Gearheart, B. Arazi and E. C. Rouchka, “DNA-Based Random Number Generation in Security Circuitry,” Biosystems, Vol. 100, No. 3, 2010, pp. 208-214.
http://dx.doi.org/10.1016/j.biosystems.2010.03.005

[15]   O. O. Babatunde, “On Pseudorandom Number Generation from Programmable and Computable Biomolecules: Deoxyribonucleic (DNA) as a Novel Pseudorandom Number Generator,” World Applied Programming, Vol. 1, No. 3, 2011, pp. 215-227.

[16]   G. C. Sirakoulis, “Hybrid DNA Cellular Automata for Pseudorandom Number Generation,” 2012 International Conference on High Performance Computing and Simulation (HPCS), Madrid, 2-6 July 2012, pp. 238-244.
http://dx.doi.org/10.1109/HPCSim.2012.6266918

[17]   Y. P. Zhang, Y. Zhu, Z. Wang and R. O. Sinnott, “Index-Based Symmetric DNA Encryption Algorithm, The 4th International Congress on Image and Signal Processing, Shanghai, 15-17 October 2011.
http://dtl.unimelb.edu.au/researchfile287042.pdf

[18]   Y. P. Zhang, L. He and B. C. Fu, “Research on DNA Cryptography, Applied Cryptography and Network Security,” InTech Press, 2012.
http://www.intechopen.com/books/applied-cryptography-and-network-security/research-on-dna-cryptography

[19]   E. Lieberman-Aiden, et al., “Comprehensive Mapping of Long-Range Interactions Reveals Folding Principles of the Human Genome,” Science, Vol. 326, No. 5950, 2009. pp. 289-293. http://dx.doi.org/10.1126/science.1181369

[20]   M. B. Gerstein, A. Kundaje, M. Hariharan, et al., “Architecture of the Human Regulatory Network Derived from ENCODE data,” Nature, Vol. 489, No. 7414, 2012, pp. 91-100. http://dx.doi.org/10.1038/nature11245

[21]   W. F. Doolittle, “Is Junk DNA Bunk? A Critique of ENCODE,” Proceedings of the National Academy of Sciences, Vol. 110, No. 14, 2013, p. 5294.

[22]   J. M. Engreitz, A. Pandya-Jones, P. McDonel, et al., “Large Noncoding RNAs Can Localize to Regulatory DNA Targets by Exploriting the 3D Architecture of the Genome,” 2013.

[23]   K. Sakamoto, “Molecular Computation by DNA Hairpin Formation,” Science, Vol. 288, No. 5469, 2000, pp. 1223-1226. http://dx.doi.org/10.1126/science.288.5469.1223

[24]   A. Arneodo, C. Vaillant. et al., “Multi-Scale Coding of Genomic Information: From DNA Sequence to Genome Structure and Function,” Physics Reports, Vol. 498, No. 2, 2011, pp. 45-188.
http://dx.doi.org/10.1016/j.physrep.2010.10.001

[25]   S. Engela, A. Alemany and N. Forns, “Folding and Unfolding of a Triple-Branch DNA Molecule with Four Conformational States,” Philosophical Magazine, Vol. 91, No. 13, 2011, pp. 2049-2065.
http://dx.doi.org/10.1080/14786435.2011.557671

[26]   J. M. Urquiza, I. Rojas, et al., “Method for Prediction of Protein-Protein Interactions in Yeast Using Genomics/ Proteomics Information and Feature Selection,” Neurocomputing, Vol. 74, No. 16, 2011, pp. 2683-2690.
http://dx.doi.org/10.1016/j.neucom.2011.03.025

[27]   H. Y. Zhang and X. Y. Liu. “A CLIQUE Algorithm Using DNA Computing Techniques Based on Closed-Circle DNA Sequences,” Biosystems, Vol. 105, No. 1, 2011, pp. 73-82. http://dx.doi.org/10.1016/j.biosystems.2011.03.004

[28]   B. Banfai, H. Jia, J. Khatun, et al., “Long Noncoding RNAs Are Rarely Translated in Two Human Cell Lines,” Genome Research, Vol. 22, No. 9, 2012, pp. 1646-1657.
http://dx.doi.org/10.1101/gr.134767.111

[29]   J. S. Wang and M. Yan, “Numerical Methods in Bioinformatics,” Science Press, Beijing, 2013.

[30]   N. A. Tchurikov, O. V. Kretova, D. M. Fedoseeva, et al., “DNA Double-Strand Breaks Coupled with PARP1 and HNRNPA2B1 Binding Sites Flank Coordinately Expressed Domains in Human Chromosomes,” PLoS Genetics, Vol. 9, No. 4, 2013, Article ID: e1003429.
http://dx.doi.org/10.1371/journal.pgen.1003429

[31]   J. Z. J. Zheng and C. H. Zheng, “A Framework to Express Variant and Invariant Functional Spaces for Binary Logic,” Frontier of Electrical and Electronic Engineering in China, Vol. 5, No. 2, 2010, pp. 163-172.
http://dx.doi.org/10.1007/s11460-010-0011-4

[32]   J. Zheng, C. Zheng and T. Kunii, “A Framework of Variant Logic Construction for Cellular Automata,” In: A. Salcido, Ed., Cellular Automata—Innovative Modelling for Science and Engineering, InTech Press, 2011, pp. 325-352. http://www.intechopen.com/chapters/20706

[33]   Q. P. Li and J. Zheng, “2D Spatial Distributions for Measures of Random Sequences Using Conjugate Maps,” Proceedings of the 11th Australian Information Warfare and Security Conference, Perth, 2010.
http://ro.ecu.edu.au/isw/34

[34]   J. Zheng, C. Zheng and T. Kunii, “Interactive Maps on Variant Phase Spaces—From Measurements Micro Ensembles to Ensemble Matrices on Statistical Mechanics of Particle Models,” In: A. Salcido, Ed., Emerging Application of Cellular Automata, InTech Press, 2013, pp. 113-196. http://dx.doi.org/10.5772/51635

[35]   J. Zheng, “Novel Pseudo-Random Number Generation Using Variant Logic Framework,” The 2nd International Cyber Resilience Conference, Perth, 1-2 August 2011, pp. 100-104.
http://igneous.scis.ecu.edu.au/proceedings/2011/icr/zheng.pdf

[36]   W. Z. Yang and J. Z. J. Zheng, “PRNG Based on Variant Logic,” 7th International ICST Conference on Communications and Networking in China (CHINACOM 2012), Kunming, 8-10 August 2012, pp. 202-205.
http://www.computer.org/csdl/proceedings/chinacom/2012/2698/00/06417476-abs.html

[37]   W. Z. Yang and J. Zheng, “Variant Pseudo-Random Number Generator,” Hakin9 Extra, No. 6, 2012, pp. 28-31.
http://hakin9.org/hakin9-extra-62012/

[38]   W.Q. Zhang and J. Zheng, “Randomness Measurement of Pseudorandom Sequence Using Different Generation Mechanisms and DNA Sequence,” Journal of Chengdu University of Information Technology, Vol. 27, No. 6, 2012, pp. 548-555.

 
 
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