Optimization and Applications in Bioinformatics

Most of bioinformatics problems deal with the manipulation of large sets of variables. Hence, looking for a good combinaisons of these variables requires advanced search mechanisms. The aim of this tutorial is to provide hints on how to use combinatorial optimization to help with bioinformatics challenges. The first part of the tutorial will be dedicated to the combinatorial optimization domain. It will focuss on the key concepts (modelization of problems, definition of the objective function, determination of the constraints) and will present some classical solution methods including exact methods and metaheuristics such as genetic algorithms. The second part of the tutorial will present some applications. It will illustrate through different bioinformatics problems, how combinatorial optimization approaches have been applied with success.