Abstract
Encoding and processing information in DNA-, RNA- and other biomolecule-based devices is an important topic in DNA-based computing with potentially important applications to fields such as bioinformatics, and, conceivably, microbiology and genetics. New methods to encode large data sets compactly on DNA chips has been recently proposed in (Garzon & Deaton, 2004) [18]. The method consists of shredding the data into short oligonucleotides and pouring it over a DNA chip with spots populated by copies of a basis set of noncrosshybridizing strands. In this paper, we provide an analysis of the sensitivity, robustness, and capacity of the encodings. First, we provide preliminary experimental evidence of the degree of variability of the representation and show that it can be made robust despite reaction conditions and the uncertainty of the hybridization chemistry in vitro. Based on these simulations, we provide an empirical estimate of the capacity of the representation to store information. Second, we present a new theoretical model to analyze and estimate the sensitivity and capacity of a given DNA chip for information discrimination. Finally, we briefly discuss some potential applications, such as genomic analysis, classification problems, and data mining of massive amounts of data in abiotic form without the onerous cost of massive synthesis of DNA strands.
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Baum, E.: Building an associative memory vastly larger than the brain. Science 268, 583–585 (1995)
Bi, H., Chen, J., Deaton, R., Garzon, M., Rubin, H., Wood, D.: A PCR-based Protocol for In Vitro Selection of Non-Crosshybridizing Oligonucleotides. J. of Natural Computing (2003)
Blain, D., Garzon, M.: Simulation tools for biomolecular computing. In: Garzon, Rose (eds.), vol. 3(4), pp. 117–129 (2004)
Chen, J., Deaton, R., Garzon, M., Kim, J.W., Wood, D.H., Bi, H., Carpenter, D., Le, J.S., Wang, Y.Z.: Sequence complexity of large libraries of dna oligonucleotides. In: These Proceedings (2005)
Chen, J., Deaton, R., Garzon, M., Wood, D.H., Bi, H., Carpenter, D., Wang, Y.Z.: Characterization of Non-Crosshybridizing DNA Oligonucleotides Manufactured in vitro. In: Ferretti, C., Mauri, G., Zandron, C. (eds.) DNA 2004. LNCS, vol. 3384, pp. 50–61. Springer, Heidelberg (2005)
Deaton, R., Chen, J., Bi, H., Rose, J.: A software tool for generating non-crosshybridizing libraries of dna oligonucleotides. In: [14], pp. 252–261 (2002)
Deaton, R.J., Chen, J., Bi, H., Garzon, M., Rubin, H., Wood, D.H.: A PCR-based protocol for in vitro selection of non-crosshybridizing oligonucleotides. In: Hagiya, Ohuchi (eds.), pp. 105–114 (2002a)
Garzon, M., Bobba, K., Hyde, B.: Digital information encoding on DNA. In: Bressan, S., Chaudhri, A.B., Li Lee, M., Yu, J.X., Lacroix, Z. (eds.) CAiSE 2002 and VLDB 2002. LNCS, vol. 2590, pp. 151–166. Springer, Heidelberg (2003b)
Garzon, M., Deaton, R., Neathery, P., Murphy, R.C., Franceschetti, D.R., Stevens Jr., E.: On the encoding problem for DNA computing. In: Preliminary Proceedings of the Third DIMACS Workshop on DNA-based Computing, U of Pennsylvania, pp. 230–237 (1997)
Garzon, M., Neathery, P.I., Deaton, R., Murphy, R.C., Franceschetti, D.R., Stevens Jr., S.E.: A new metric for DNA computing. In: Koza, et al. (eds.), pp. 472–478 (1997a)
Garzon, M., Neel, A., Bobba, K.: Efficiency and reliability of semantic retrieval in DNA-based memories, pp. 157–169 (2003)
Garzon, M., Phan, V., Bobba, K., Kontham, R.: Sensitivity Analysis of Microaary Data: A New Approach. In: Proc. IBE Conference, Athens GA. Biotechnology Press (2005)
Garzon, M., Rose, J.: Simulation Tools for Biomolecular Computing. Special Issue of the Journal of Natural Computing 4(3) (2004)
Hagiya, M., Ohuchi, A. (eds.): DNA 2002. LNCS, vol. 2568. Springer, Heidelberg (2003)
Head, T., Yamamura, M., Gal, S.: Aqueous computing: Writing on molecules. In: Proceedings of the Congress on Evolutionary Computing (CEC 1999) (1999)
Head, T., Yamamura, M., Gal, S.: Relativized code concepts and multi-tube DNA dictionaries. In: Finite vs Infinite: COntrobutions to an eternal dilemma (Discrete math and Theoretical Computer Science), pp. 175–186 (2001)
Garzon, M., Blain, D., Neel, A.: Virtual test tubes for biomolecular computing. In: Garzon, Rose (eds.), vol. 3(4), pp. 460–477 (2004)
Garzon, M., Deaton, R.: Codeword Design and Information Encoding in DNA Ensembles. J. of Natural Computing 3(4), 253–292 (2004)
Mount, D.: Bioinformatics: Sequence and genome analysis. Spring Harbor Lab Press, MD (2001)
Phan, V., Garzon, M.: Information encoding using DNA. In: Proc. 10th Int. Conf. on DNA Computing DNA10 (2004)
Stekel, D.: Microarray Bioinformatics. Cambridge University Press, Cambridge (2003)
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Garzon, M.H., Phan, V., Bobba, K.C., Kontham, R. (2006). Sensitivity and Capacity of Microarray Encodings. In: Carbone, A., Pierce, N.A. (eds) DNA Computing. DNA 2005. Lecture Notes in Computer Science, vol 3892. Springer, Berlin, Heidelberg. https://doi.org/10.1007/11753681_7
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DOI: https://doi.org/10.1007/11753681_7
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