Circular inversions of permutations and their use in sorting problems

Предлагается алгоритм сортировки перестановки на основе её множеств круговых инверсий. Указывается на приложения в молекулярной биологии и в теории групп подстановок

Packing edge-disjoint cycles in graphs and the cyclomatic number

For a graph G let \mu (G) denote the cyclomatic number and let \nu (G) denote the maximum number of edge-disjoint cycles of G. We prove that for every k \geq 0 there is a nite set P(k) such that every 2-connected graph G for which \mu (G) - \nu (G) = k arises by applying a simple extension rule to a graph in P(k). Furthermore, we determine P(k) for k \leq 2 exactly

Median clouds and a fast transposition median solver

The median problem seeks a permutation whose total distance to a given set of permutations (the base set) is minimal. This is an important problem in comparative genomics and has been studied for several distance measures such as reversals. The transposition distance is less relevant biologically, but it has been shown that it behaves similarly to the most important biological distances, and can thus give important information on their properties. We have derived an algorithm which solves the transposition median problem, giving all transposition medians (the median cloud). We show that our algorithm can be modified to accept median clouds as elements in the base set and briefly discuss the new concept of median iterates (medians of medians) and limit medians, that is the limit of this iterate

Sorting by Prefix Block-Interchanges

We initiate the study of sorting permutations using prefix block-interchanges, which exchange any prefix of a permutation with another non-intersecting interval. The goal is to transform a given permutation into the identity permutation using as few such operations as possible. We give a 2-approximation algorithm for this problem, show how to obtain improved lower and upper bounds on the corresponding distance, and determine the largest possible value for that distance

Multiple genome rearrangement by swaps and by element duplications

AbstractWe consider the swap distance and the element duplication distance. We show that the swap centre permutation problem is NP-complete. We show that the element duplication centre problem is NP-complete

Weighted Minimum-Length Rearrangement Scenarios

We present the first known model of genome rearrangement with an arbitrary real-valued weight function on the rearrangements. It is based on the dominant model for the mathematical and algorithmic study of genome rearrangement, Double Cut and Join (DCJ). Our objective function is the sum or product of the weights of the DCJs in an evolutionary scenario, and the function can be minimized or maximized. If the likelihood of observing an independent DCJ was estimated based on biological conditions, for example, then this objective function could be the likelihood of observing the independent DCJs together in a scenario. We present an O(n^4)-time dynamic programming algorithm solving the Minimum Cost Parsimonious Scenario (MCPS) problem for co-tailed genomes with n genes (or syntenic blocks). Combining this with our previous work on MCPS yields a polynomial-time algorithm for general genomes. The key theoretical contribution is a novel link between the parsimonious DCJ (or 2-break) scenarios and quadrangulations of a regular polygon. To demonstrate that our algorithm is fast enough to treat biological data, we run it on syntenic blocks constructed for Human paired with Chimpanzee, Gibbon, Mouse, and Chicken. We argue that the Human and Gibbon pair is a particularly interesting model for the study of weighted genome rearrangements