String Processing and Information Retrieval

My purpose in this text is to highlight some of the most important challenges in the area of Bioinformatics, drawing from several sources. The field is already pretty large and becoming more so. Therefore the selection of challenges presented here will tend to focus on topics I am more familiar with, with only brief mentions of topics I do not know in depth. The challenges vary in scope and motivation: some are broad, abstract while others are specialized to a given topic. Some are biologically motivated, others are nice as computer science problems. Also, I tried to show the dependencies among the challenges in order to get a global picture of the area. A basic knowledge on the principles of computational biology is assumed.