Bioinformatics Algorithms

The sequencing of the human genome a decade ago fueled a computational revolution in biology, which has arguably been an impetus for more new algorithms than any other fundamental realm of science. The newly formed links between computer science and biology affect the way we teach computational ideas to biologists, as well as how applied algorithms are taught to computer scientists. Genome sequencing is just one of hundreds of biological problems that have become inextricable from the computational methods required to solve them. In this course, we will take a look at some of the algorithmic ideas that are fundamental to an understanding of modern biology. Computational concepts like dynamic programming and graph theory will help us explore algorithms applied to a wide range of biological topics, from finding regulatory motifs to reconstructing the tree of life. Throughout the process, we will apply real bioinformatics algorithms to real genetic data.

This book is about how to design algorithms that solve biological problems. We will see how popular bioinformatics algorithms work and we will see what principles drove their design.

This book constitutes the refereed proceedings of the Second International Workshop on Algorithms and Computation, WALCOM 2008, held in Dhaka, Bangladesh, in February 2008.