Rank-Modulation Codes for DNA Storage With Shotgun Sequencing

Synthesis of DNA molecules offers unprecedented advances in storage technology. Yet, the microscopic world in which these molecules reside induces error patterns that are fundamentally different from their digital counterparts. Hence, to maintain reliability in reading and writing, new coding schemes must be developed. In a reading technique called shotgun sequencing, a long DNA string is read in a sliding window fashion, and a profile vector is produced. It was recently suggested by Kiah et al. that such a vector can represent the permutation which is induced by its entries, and hence a rank-modulation scheme arises. Although this interpretation suggests high error tolerance, it is unclear which permutations are feasible and how to produce a DNA string whose profile vector induces a given permutation. In this paper, by observing some necessary conditions, an upper bound for the number of feasible permutations is given. Furthermore, a technique for deciding the feasibility of a permutation is devised. By using insights from this technique, an algorithm for producing a considerable number of feasible permutations is given, which applies to any alphabet size and any window length

Rank-Modulation Codes for DNA Storage With Shotgun Sequencing

Synthesis of DNA molecules offers unprecedented advances in storage technology. Yet, the microscopic world in which these molecules reside induces error patterns that are fundamentally different from their digital counterparts. Hence, to maintain reliability in reading and writing, new coding schemes must be developed. In a reading technique called shotgun sequencing, a long DNA string is read in a sliding window fashion, and a profile vector is produced. It was recently suggested by Kiah et al. that such a vector can represent the permutation which is induced by its entries, and hence a rank-modulation scheme arises. Although this interpretation suggests high error tolerance, it is unclear which permutations are feasible and how to produce a DNA string whose profile vector induces a given permutation. In this paper, by observing some necessary conditions, an upper bound for the number of feasible permutations is given. Furthermore, a technique for deciding the feasibility of a permutation is devised. By using insights from this technique, an algorithm for producing a considerable number of feasible permutations is given, which applies to any alphabet size and any window length

Algorithmes d'approximation à mémoire limitée pour le traitement de grands graphes (le problème du Vertex Cover)

Nous nous sommes intéressés à un problème d'optimisation sur des graphes (le problème du Vertex Cover) dans un contexte bien particulier : celui des grandes instances de données. Nous avons défini un modèle de traitement se basant sur trois contraintes (en relation avec la quantité de mémoire limitée, par rapport à la grande masse de données à traiter) et qui reprenait des propriétés issus de plusieurs modèles existants. Nous avons étudié plusieurs algorithmes adaptés à ce modèle. Nous avons analysé, tout d'abord de façon théorique, la qualité de leurs solutions ainsi que leurs complexités. Nous avons ensuite mené une étude expérimentale sur de gros graphes. De manière générale, les travaux menés durant cette thèse peuvent fournir des indicateurs pour choisir le ou les algorithmes qui conviennent le mieux pour traiter le problème du vertex cover sur de gros graphes. Choisir un algorithme (qui plus est d'approximation) qui soit à la foisperformant (en terme de qualité de solution et de complexité) et qui satisfasse les contraintes du modèle que l'on considère est délicat. en effet, les algorithmes les plus performants ne sont pas toujours les mieux adaptés. dans les travaux que nous avons réalisés, nous sommes parvenus à la conclusion qu'il est préférable de choisir au départ l'algorithme qui est le mieux adapté plutôt que de choisir celui qui est le plus performant.We are interested to an optimization problem on graphs (the Vertex Cover problem) in a very specific context : the huge instances of data. We defined a treatment model based on three constraints (in connection with the limited amount of memory compared to the huge amount of data to be processed) and that reproduces properties from several existing models. We studied several algorithms adapted to this model. We examined, first theoretically, their solutions quality and their complexities. We then conducted an experimental study on large graphs. In general, the work made during this thesis may provide indicators for select algorithms that are best suited to resolve the Vertex Cover problem on large graphs. Choose an algorithm (which is approximated) that is both efficient (in terms of quality of solution and complexity) and satisfies the constraints model whether we consider is tricky. in fact, the most efficient algorithms are not always the best adapted. In the work we have done, we reached the conclusion that, at the beginning, it is best to choose the best suited algorithm rather than the more efficient.EVRY-Bib. électronique (912289901) / SudocSudocFranceF