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The ability to store data in the DNA of a living organism has applications in a variety of areas including synthetic biology and watermarking of patented genetically modified organisms. Data stored in this medium are subject to errors arising from various mutations, such as point mutations, indels, and tandem duplication, which need to be corrected to maintain data integrity. In this paper, we provide error-correcting codes for errors caused by tandem duplications, which create a copy of a block of the sequence and insert it in a tandem manner, i.e., next to the original. In particular, we present two families of codes for correcting errors due to tandem duplications of a fixed length: the first family can correct any number of errors, while the second corrects a bounded number of errors. We also study codes for correcting tandem duplications of length up to a given constant $k$ , where we are primarily focused on the cases of $k=2,3$ . Finally, we provide a full classification of the sets of lengths allowed in tandem duplication that result in a unique root for all sequences. [ABSTRACT FROM AUTHOR]

We study the rate-distortion relationship in the set of permutations endowed with the Kendall $\tau $ -metric and the Chebyshev metric (the $\ell _\infty $ -metric). This paper is motivated by the application of permutation rate-distortion to the average-case and worst-case distortion analysis of algorithms for ranking with incomplete information and approximate sorting algorithms. For the Kendall $\tau $ -metric, we provide bounds for various distortion regimes, while for the Chebyshev metric, we present bounds that are valid for all distortions and are especially accurate for small distortions. In addition, for the Chebyshev metric, we provide a construction for covering codes. [ABSTRACT FROM AUTHOR]

We address the problem of multipermutation code design in the Ulam metric for novel storage applications. Multipermutation codes are suitable for flash memory where cell charges may share the same rank. Changes in the charges of cells manifest themselves as errors whose effects on the retrieved signal may be measured via the Ulam distance. As part of our analysis, we study multipermutation codes in the Hamming metric, known as constant composition codes. We then present bounds on the size of multipermutation codes and their capacity, for both the Ulam and the Hamming metrics. Finally, we present constructions and accompanying decoders for multipermutation codes in the Ulam metric. [ABSTRACT FROM PUBLISHER]

We consider rank modulation codes for flash memories that allow for handling arbitrary charge-drop errors. Unlike classical rank modulation codes used for correcting errors that manifest themselves as swaps of two adjacently ranked elements, the proposed translocation rank codes account for more general forms of errors that arise in storage systems. Translocations represent a natural extension of the notion of adjacent transpositions and as such may be analyzed using related concepts in combinatorics and rank modulation coding. Our results include derivation of the asymptotic capacity of translocation rank codes, construction techniques for asymptotically good codes, as well as simple decoding methods for one class of constructed codes. As part of our exposition, we also highlight the close connections between the new code family and permutations with short common subsequences, deletion and insertion error-correcting codes for permutations, and permutation codes in the Hamming distance. [ABSTRACT FROM PUBLISHER]

The "Japanese" theorem is extended to multiple multicast sessions in an arbitrary network to characterize the routing capacity region by the intersection of an infinite collection of half-spaces. An elimination technique is developed to simplify this infinite description into a finite one based upon the shortest routing paths and trees in the network graph. This result is used as a step in providing the capacity regions for two multimessage multicast problems on undirected ring networks; in the first case only unicast and broadcast sessions are considered, and in the second case multicast sessions where the source and destination vertices form lines of adjacent vertices are studied. Network coding is generally necessary to achieve network capacity, but for our multimessage multicast problems, new arguments are used to demonstrate that routing can achieve network coding bounds. [ABSTRACT FROM AUTHOR]