Abstract
Information encoding and processing in DNA has proved to be an important problem for biomolecular computing, including the well studied codeword design problem. A lower bound is established for the capacity of DNA to encode information using a combinatorial model of DNA homology given by the so-called h-distance. This bound decreases exponentially with a parameter τ that roughly codes for stringency in reaction conditions. We further introduce a new family of near-optimal codeword sets, so-called shuffle codes. This construction, which is optimal in terms of efficiency, can also be used to produce set of codewords with a given constant GC-content. These codes yield estimates of the capacity of DNA oligonucleotides to store abiotic information in DNA arrays as defined in [11]. Finally, we discuss the sensitivity of the corresponding DNA chip encodings to store and discriminate inputs, including the regions of maximum discrimination and uncertainty.
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Phan, V., Garzon, M.H. (2005). The Capacity of DNA for Information Encoding. In: Ferretti, C., Mauri, G., Zandron, C. (eds) DNA Computing. DNA 2004. Lecture Notes in Computer Science, vol 3384. Springer, Berlin, Heidelberg. https://doi.org/10.1007/11493785_25
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DOI: https://doi.org/10.1007/11493785_25
Publisher Name: Springer, Berlin, Heidelberg
Print ISBN: 978-3-540-26174-2
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