Codes for DNA Storage Channels
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Publication:6256002
arXiv1410.8837MaRDI QIDQ6256002FDOQ6256002
Gregory J. Puleo, Olgica Milenkovic, Han Mao Kiah
Publication date: 31 October 2014
Abstract: We consider the problem of assembling a sequence based on a collection of its substrings observed through a noisy channel. The mathematical basis of the problem is the construction and design of sequences that may be discriminated based on a collection of their substrings observed through a noisy channel. We explain the connection between the sequence reconstruction problem and the problem of DNA synthesis and sequencing, and introduce the notion of a DNA storage channel. We analyze the number of sequence equivalence classes under the channel mapping and propose new asymmetric coding techniques to combat the effects of synthesis and sequencing noise. In our analysis, we make use of restricted de Bruijn graphs and Ehrhart theory for rational polytopes.
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