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- W2741838265 abstract "In this dissertation, we address some of the algorithmic and computational issues involved in computational biology problems. In particular, we give new algorithms for three different problems, viz., restriction site mapping, reconstructing DNA strings from sequencing by hybridization (SBH) data, and subgraph detection algorithms.We propose new, practical algorithms which resolve the noisy experimental data from DNA partial digests, including the possibility of missing fragments. We analyze the performance of these algorithms under a reasonable probability distribution, establishing a relative error limit of r = $Theta$(1/$nsp2$) beyond which our technique becomes infeasible. Through simulations, we establish that our technique is robust enough to reconstruct data with relative errors of up to 7.0% in the measured fragment lengths for typical problems.Sequencing by hybridization is a new approach to DNA sequencing in which we sequence the DNA by asking all substring queries of length m, using a sequencing chip C(m). We develop a theory of interactive sequencing by hybridization, based on reconstructing strings from substrings. We provide tight bounds on the complexity of reconstructing unknown strings from substring queries. Specifically, we show that $Theta({n}alpha)$ substring queries are necessary and sufficient, where $alpha$ is the alphabet size. We also demonstrate that subsequence queries are more efficient by showing O(n lg $alpha$) queries are necessary and sufficient. We give algorithms to build decision trees which are within a constant factor of an optimal decision tree with the constant depending upon $alpha$.Finally, we consider the problem of subgraph isomorphism which has applications in fragment assembly and other DNA sequencing algorithms. We present general algorithms for fixed-subgraph isomorphism which improve or unify previous results. In particular, we present an $O(nsp{f}m)$ algorithm for recognizing a fixed subgraph H with flower number f within a graph G with n vertices and m edges. (Abstract shortened by UMI.)" @default.
- W2741838265 created "2017-08-08" @default.
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- W2741838265 date "1993-01-11" @default.
- W2741838265 modified "2023-09-23" @default.
- W2741838265 title "Combinatorial algorithms for computational biology" @default.
- W2741838265 hasPublicationYear "1993" @default.
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