A quantitative analysis of secondary RNA structure using domination based parameters on trees

BACKGROUND: It has become increasingly apparent that a comprehensive database of RNA motifs is essential in order to achieve new goals in genomic and proteomic research. Secondary RNA structures have frequently been represented by various modeling methods as graph-theoretic trees. Using graph theory as a modeling tool allows the vast resources of graphical invariants to be utilized to numerically identify secondary RNA motifs. The domination number of a graph is a graphical invariant that is sensitive to even a slight change in the structure of a tree. The invariants selected in this study are variations of the domination number of a graph. These graphical invariants are partitioned into two classes, and we define two parameters based on each of these classes. These parameters are calculated for all small order trees and a statistical analysis of the resulting data is conducted to determine if the values of these parameters can be utilized to identify which trees of orders seven and eight are RNA-like in structure. RESULTS: The statistical analysis shows that the domination based parameters correctly distinguish between the trees that represent native structures and those that are not likely candidates to represent RNA. Some of the trees previously identified as candidate structures are found to be "very" RNA like, while others are not, thereby refining the space of structures likely to be found as representing secondary RNA structure. CONCLUSION: Search algorithms are available that mine nucleotide sequence databases. However, the number of motifs identified can be quite large, making a further search for similar motif computationally difficult. Much of the work in the bioinformatics arena is toward the development of better algorithms to address the computational problem. This work, on the other hand, uses mathematical descriptors to more clearly characterize the RNA motifs and thereby reduce the corresponding search space. These preliminary findings demonstrate that graph-theoretic quantifiers utilized in fields such as computer network design hold significant promise as an added tool for genomics and proteomics

Random subgraphs make identification affordable

An identifying code of a graph is a dominating set which uniquely determines all the vertices by their neighborhood within the code. Whereas graphs with large minimum degree have small domination number, this is not the case for the identifying code number (the size of a smallest identifying code), which indeed is not even a monotone parameter with respect to graph inclusion. We show that every graph $G$ with $n$ vertices, maximum degree $\Delta=\omega(1)$ and minimum degree $\delta\geq c\log{\Delta}$, for some constant $c>0$, contains a large spanning subgraph which admits an identifying code with size $O\left(\frac{n\log{\Delta}}{\delta}\right)$. In particular, if $\delta=\Theta(n)$, then $G$ has a dense spanning subgraph with identifying code $O\left(\log n\right)$, namely, of asymptotically optimal size. The subgraph we build is created using a probabilistic approach, and we use an interplay of various random methods to analyze it. Moreover we show that the result is essentially best possible, both in terms of the number of deleted edges and the size of the identifying code

Reformulação de Estratégia de Aliança Defensiva e Ofensiva em Grafos

Neste trabalho é proposto um novo problema chamado de reformulação de estratégia de alianças, onde a aliança defensiva se transforma em uma aliança ofensiva que contém os vértices da aliança defensiva de origem, e vice-versa. O objetivo é reformular a estratégia de aliança defensiva e ofensiva de cardinalidade mínima para algumas classes de grafos como caminhos, ciclos, rodas, grafos completos, bipartidos completos, estrela e árvores binárias balanceadas

On the size of identifying codes in triangle-free graphs

In an undirected graph $G$, a subset $C\subseteq V(G)$ such that $C$ is a dominating set of $G$, and each vertex in $V(G)$ is dominated by a distinct subset of vertices from $C$, is called an identifying code of $G$. The concept of identifying codes was introduced by Karpovsky, Chakrabarty and Levitin in 1998. For a given identifiable graph $G$, let \M(G) be the minimum cardinality of an identifying code in $G$. In this paper, we show that for any connected identifiable triangle-free graph $G$ on $n$ vertices having maximum degree $\Delta\geq 3$, \M(G)\le n-\tfrac{n}{\Delta+o(\Delta)}. This bound is asymptotically tight up to constants due to various classes of graphs including $(\Delta-1)$-ary trees, which are known to have their minimum identifying code of size $n-\tfrac{n}{\Delta-1+o(1)}$. We also provide improved bounds for restricted subfamilies of triangle-free graphs, and conjecture that there exists some constant $c$ such that the bound \M(G)\le n-\tfrac{n}{\Delta}+c holds for any nontrivial connected identifiable graph $G$

Alliance free sets in Cartesian product graphs

Let $G=(V,E)$ be a graph. For a non-empty subset of vertices $S\subseteq V$, and vertex $v\in V$, let $\delta_S(v)=|\{u\in S:uv\in E\}|$ denote the cardinality of the set of neighbors of $v$ in $S$, and let $\bar{S}=V-S$. Consider the following condition: {equation}\label{alliancecondition} \delta_S(v)\ge \delta_{\bar{S}}(v)+k, \{equation} which states that a vertex $v$ has at least $k$ more neighbors in $S$ than it has in $\bar{S}$. A set $S\subseteq V$ that satisfies Condition (\ref{alliancecondition}) for every vertex $v \in S$ is called a \emph{defensive} $k$-\emph{alliance}; for every vertex $v$ in the neighborhood of $S$ is called an \emph{offensive} $k$-\emph{alliance}. A subset of vertices $S\subseteq V$, is a \emph{powerful} $k$-\emph{alliance} if it is both a defensive $k$-alliance and an offensive $(k +2)$-alliance. Moreover, a subset $X\subset V$ is a defensive (an offensive or a powerful) $k$-alliance free set if $X$ does not contain any defensive (offensive or powerful, respectively) $k$-alliance. In this article we study the relationships between defensive (offensive, powerful) $k$-alliance free sets in Cartesian product graphs and defensive (offensive, powerful) $k$-alliance free sets in the factor graphs

On the complement graph and defensive k-alliances

AbstractIn this paper, we obtain several tight bounds of the defensive k-alliance number in the complement graph from other parameters of the graph. In particular, we investigate the relationship between the alliance numbers of the complement graph and the minimum and maximum degree, the domination number and the isoperimetric number of the graph. Moreover, we prove the NP-completeness of the decision problem underlying the defensive k-alliance number