Abstract
The gene order on a chromosome is a necessary data for most comparative genomics studies, but in many cases only partial orders can be obtained by current genetic mapping techniques. The Minimum Breakpoint Linearization Problem aims at constructing a total order from this partial knowledge, such that the breakpoint distance to a reference genome is minimized. In this paper, we first expose a flaw in two algorithms formerly known for this problem [4,2]. We then present a new modeling for this problem, and use it to design three approximation algorithms, with ratios resp. O(log(k)loglog(k)), O(log2(|X|)) and m 2 + 4m − 4, where k is the optimal breakpoint distance we look for, |X| is upper bounded by the number of pair of genes for which the partial order is in contradiction with the reference genome, and m is the number of genetic maps used to create the input partial order.
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Bulteau, L., Fertin, G., Rusu, I. (2010). Revisiting the Minimum Breakpoint Linearization Problem. In: Kratochvíl, J., Li, A., Fiala, J., Kolman, P. (eds) Theory and Applications of Models of Computation. TAMC 2010. Lecture Notes in Computer Science, vol 6108. Springer, Berlin, Heidelberg. https://doi.org/10.1007/978-3-642-13562-0_16
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DOI: https://doi.org/10.1007/978-3-642-13562-0_16
Publisher Name: Springer, Berlin, Heidelberg
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