Abstract
Given two genomes, the problem of sorting by reversals is to explain the evolution of these genomes from a common ancestor by a minimal sequence of reversals. The Hannenhalli and Pevzner (HP) algorithm [8] gives the reversal distance and outputs one possible sequence of reversals. However, there is usually a very large set of such minimal solutions. To really understand the mechanism of reversals, it is important to have access to that set of minimal solutions. We develop a new method that allows the user to choose one or several solutions, based on different criteria. In particular, it can be used to sort genomes by weighted reversals. This requires a characterization of all “safe” reversals, as defined in the HP theory. We describe a procedure that outputs the set of all safe reversals at each step of the sorting procedure in time O(n 3), and we show how to characterize a large set of such reversals in a more efficient way. We also describe a linear algorithm allowing to generate a random genome of a given reversal distance. We use our methods to verify the hypothesis that, in bacteria, most reversals act on segments surrounding one of the two endpoints of the replication axis [12].
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Ajana, Y., Jean-François, L., Tillier, E.R., El-Mabrouk, N. (2002). Exploring the Set of All Minimal Sequences of Reversals — An Application to Test the Replication-Directed Reversal Hypothesis. In: Guigó, R., Gusfield, D. (eds) Algorithms in Bioinformatics. WABI 2002. Lecture Notes in Computer Science, vol 2452. Springer, Berlin, Heidelberg. https://doi.org/10.1007/3-540-45784-4_23
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DOI: https://doi.org/10.1007/3-540-45784-4_23
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