On the chromatic number of the \u3cem\u3eAO\u3c/em\u3e(2, \u3cem\u3ek \u3c/em\u3e, \u3cem\u3ek\u3c/em\u3e-1) graphs.

The alphabet overlap graph is a modification of the well known de Bruijn graph. De Bruijn graphs have been highly studied and hence many properties of these graphs have been determined. However, very little is known about alphabet overlap graphs. In this work we determine the chromatic number for a special case of these graphs. We define the alphabet overlap graph by G = AO(a, k, t, where a, k and t are positive integers such that 0 ≤ t ≤ k. The vertex set of G is the set of all k-letter sequences over an alphabet of size a. Also there is an edge between vertices u, v if and only if the last t letters in u match the first t letters in v or the first t letters in u match the last t letters in v. We consider the chromatic number for the AO(a, k, t graphs when k \u3e 2, t = k - 1 and a = 2

Hyper‐Heuristics and Metaheuristics for Selected Bio‐Inspired Combinatorial Optimization Problems

Many decision and optimization problems arising in bioinformatics field are time demanding, and several algorithms are designed to solve these problems or to improve their current best solution approach. Modeling and implementing a new heuristic algorithm may be time‐consuming but has strong motivations: on the one hand, even a small improvement of the new solution may be worth the long time spent on the construction of a new method; on the other hand, there are problems for which good‐enough solutions are acceptable which could be achieved at a much lower computational cost. In the first case, specially designed heuristics or metaheuristics are needed, while the latter hyper‐heuristics can be proposed. The paper will describe both approaches in different domain problems

On a graph-theoretical model for cyclic register allocation

AbstractIn the process of compiling a computer programme, we consider the problem of allocating variables to registers within a loop. It can be formulated as a coloring problem in a circular arc graph (intersection graph of a family F of intervals on a circle). We consider the meeting graph of F introduced by Eisenbeis, Lelait and Marmol. Proceedings of the Fifth Workshop on Compilers for Parallel Computers, Malaga, June 1995, pp. 502–515. Characterizations of meeting graphs are developed and their basic properties are derived with graph theoretical arguments.Furthermore some properties of the chromatic number for periodic circular arc graphs are derived

A characterization of partial directed line graphs

Can a directed graph be completed to a directed line graph? If possible, how many arcs must be added? In this paper we address the above questions characterizing partial directed line (PDL) graphs, i.e., partial subgraph of directed line graphs. We show that for such class of graphs a forbidden configuration criterion and a Krausz's like theorem are equivalent characterizations. Furthermore, the latter leads to a recognition algorithm that requires O(m) worst case time, where m is the number of arcs in the graph. Given a partial line digraph, our characterization allows us to find a minimum completion to a directed line graph within the same time bound. The class of PDL graphs properly contains the class of directed line graphs, characterized in [J. Blazewicz, A. Hertz, D. Kobler, D. de Werra, On some properties of DNA graphs, Discrete Appl. Math. 98(1-2) (1999) 1-19], hence our results generalize those already known for directed line graphs. In the undirected case, we show that finding a minimum line graph edge completion is NP-hard. while the problem of deciding whether or not an undirected graph is a partial graph of a simple line graph is trivial. (C) 2007 Elsevier B.V. All rights reserved