The Sortability of Graphs and Matrices under Context Directed Swaps

The study of sorting permutations by block interchanges has recently been stimulated by a phenomenon observed in the genome maintenance of certain ciliate species. The result was the identification of a block interchange operation that applies only under certain constraints. Interestingly, this constrained block interchange operation can be generalized naturally to simple graphs and to an operation on square matrices. This more general context provides numerous techniques applicable to the original context. In this paper we consider the more general context, and obtain an enumeration, in closed form, of all simple graphs on n vertices that are ``sortable" by the graph analogue of the constrained version of block interchanges. We also obtain asymptotic results on the proportion of graphs on n vertices that are so sortable

Classifying Permutations under Context-Directed Swaps and the \textbf{cds} game

A special sorting operation called Context Directed Swap, and denoted \textbf{cds}, performs certain types of block interchanges on permutations. When a permutation is sortable by \textbf{cds}, then \textbf{cds} sorts it using the fewest possible block interchanges of any kind. This work introduces a classification of permutations based on their number of \textbf{cds}-eligible contexts. In prior work an object called the strategic pile of a permutation was discovered and shown to provide an efficient measure of the non-\textbf{cds}-sortability of a permutation. Focusing on the classification of permutations with maximal strategic pile, a complete characterization is given when the number of \textbf{cds}-eligible contexts is close to maximal as well as when the number of eligible contexts is minimal. A group action that preserves the number of \textbf{cds}-eligible contexts of a permutation provides, via the orbit-stabilizer theorem, enumerative results regarding the number of permutations with maximal strategic pile and a given number of \textbf{cds}-eligible contexts. Prior work introduced a natural two-person game on permutations that are not \textbf{cds}-sortable. The decision problem of which player has a winning strategy in a particular instance of the game appears to be of high computational complexity. Extending prior results, this work presents new conditions for player ONE to have a winning strategy in this combinatorial game.Comment: 22 page

A simple framework on sorting permutations

In this paper we present a simple framework to study various distance problems of permutations, including the transposition and block-interchange distance of permutations as well as the reversal distance of signed permutations. These problems are very important in the study of the evolution of genomes. We give a general formulation for lower bounds of the transposition and block-interchange distance from which the existing lower bounds obtained by Bafna and Pevzner, and Christie can be easily derived. As to the reversal distance of signed permutations, we translate it into a block-interchange distance problem of permutations so that we obtain a new lower bound. Furthermore, studying distance problems via our framework motivates several interesting combinatorial problems related to product of permutations, some of which are studied in this paper as well.Comment: 13 pages. This is the second part from division of the paper: arXiv:1411.5552v2 [math.CO], into two parts. The first part is: arXiv:1502.07674 [math.CO]. The original paper arXiv:1411.5552v2 [math.CO] will be removed soon. Comments are welcome. [v2]:Theorem 3 has been generalized to arbitrary permutation

Context Directed Reversals and the Ciliate Decryptome

Prior studies of the efficiency of the block interchange (swap) and the reversal sorting operations on (signed) permutations identified specialized versions of the these operations. These specialized operations are here called context directed reversal, abbreviated cdr, and context directed swap, abbreviated cds. Prior works have also characterized which (signed) permutations are sortable by cdr or by cds. It is now known that when a permutation is cds sortable in n steps, then any application of n consecutive applicable cds operations will sort it. Examples show that this is not the case for cdr. This phenomenon is the focus of this paper. It is proven that if a signed permutation is cdr sortable, then any cdr fixed point of it is cds sortable (the cds Rescue Theorem). The cds Rescue Theorem is discussed in the context of a mathematical model for ciliate micronuclear decryption. It is also proven that though for a given permutation the number of cdr operations leading to different cdr fixed points may be different from each other, the parity of these two numbers is the same (the cdr Parity Theorem). This result provides a solution to two previously formulated decision problems regarding certain combinatorial games.Comment: 18 pages, 13 figure

Plane permutations and applications to a result of Zagier-Stanley and distances of permutations

In this paper, we introduce plane permutations, i.e. pairs $\mathfrak{p}=(s,\pi)$ where $s$ is an $n$-cycle and $\pi$ is an arbitrary permutation, represented as a two-row array. Accordingly a plane permutation gives rise to three distinct permutations: the permutation induced by the upper horizontal ($s$), the vertical $\pi$) and the diagonal ($D_{\mathfrak{p}}$) of the array. The latter can also be viewed as the three permutations of a hypermap. In particular, a map corresponds to a plane permutation, in which the diagonal is a fixed point-free involution. We study the transposition action on plane permutations obtained by permuting their diagonal-blocks. We establish basic properties of plane permutations and study transpositions and exceedances and derive various enumerative results. In particular, we prove a recurrence for the number of plane permutations having a fixed diagonal and $k$ cycles in the vertical, generalizing Chapuy's recursion for maps filtered by the genus. As applications of this framework, we present a combinatorial proof of a result of Zagier and Stanley, on the number of $n$-cycles $\omega$, for which the product $\omega(1~2~\cdots ~n)$ has exactly $k$ cycles. Furthermore, we integrate studies on the transposition and block-interchange distance of permutations as well as the reversal distance of signed permutations. Plane permutations allow us to generalize and recover various lower bounds for transposition and block-interchange distances and to connect reversals with block-interchanges.Comment: To appear in SIAM J. Discrete Math. Considering the scope of the journal, the content in arXiv:1502.07971 "A simple framework on sorting permutations" was include

Using Ciliate Operations to construct Chromosome Phylogenies

We develop an algorithm based on three basic DNA editing operations suggested by a model for ciliate micronuclear decryption, to transform a given permutation into another. The number of ciliate operations performed by our algorithm during such a transformation is taken to be the distance between two such permutations. Applying well-known clustering methods to such distance functions enables one to determine phylogenies among the items to which the distance functions apply. As an application of these ideas we explore the relationships among the chromosomes of eight fruitfly (drosophila) species, using the well-known UPGMA algorithm on the distance function provided by our algorithm.Comment: 31 pages, 14 figures. Preliminary repor

On a lower bound for sorting signed permutations by reversals

Computing the reversal distances of signed permutations is an important topic in Bioinformatics. Recently, a new lower bound for the reversal distance was obtained via the plane permutation framework. This lower bound appears different from the existing lower bound obtained by Bafna and Pevzner through breakpoint graphs. In this paper, we prove that the two lower bounds are equal. Moreover, we confirm a related conjecture on skew-symmetric plane permutations, which can be restated as follows: let $p=(0,-1,-2,\ldots -n,n,n-1,\ldots 1)$ and let $$\tilde{s}=(0,a_1,a_2,\ldots a_n,-a_n,-a_{n-1},\ldots -a_1)$$ be any long cycle on the set $\{-n,-n+1,\ldots 0,1,\ldots n\}$. Then, $n$ and $a_n$ are always in the same cycle of the product $p\tilde{s}$. Furthermore, we show the new lower bound via plane permutations can be interpreted as the topological genera of orientable surfaces associated to signed permutations.Comment: slightly update

Sorting a Permutation by block moves

We prove a lower and an upper bound on the number of block moves necessary to sort a permutation. We put our results in contrast with existing results on sorting by block transpositions, and raise some open questions.Comment: 7 page

Permutation sorting and a game on graphs

We introduce a game on graphs. By a theorem of Zermelo, each instance of the game on a finite graph is determined. While the general decision problem on which player has a winning strategy in a given instance of the game is unsolved, we solve the decision problem for a specific class of finite graphs. This result is then applied to a permutation sorting game to prove the optimality of a proportional bound under which TWO has a winning strategy.Comment: 14 page

Quantifying CDS Sortability of Permutations by Strategic Pile Size

The special purpose sorting operation, context directed swap (CDS), is an example of the block interchange sorting operation studied in prior work on permutation sorting. CDS has been postulated to model certain molecular sorting events that occur in the genome maintenance program of some species of ciliates. We investigate the mathematical structure of permutations not sortable by the CDS sorting operation. In particular, we present substantial progress towards quantifying permutations with a given strategic pile size, which can be understood as a measure of CDS non-sortability. Our main results include formulas for the number of permutations in $\textsf{S}_n$ with maximum size strategic pile. More generally, we derive a formula for the number of permutations in $\textsf{S}_n$ with strategic pile size $k$, in addition to an algorithm for computing certain coefficients of this formula, which we call merge numbers.Comment: 19 page