Axelson-Fisk M. Comparative Gene Finding. Models, Algorithms and Implementation

Springer, 2010. — 317 p.Comparative genomics is a new and emerging field and with the explosion of available biological sequences the requests for faster, more efficien and more robust algorithms to analyze all this data are immense. This book is meant to serve as a self-contained instruction of the state-of-the-art of computational gene findin in general and of comparative approaches in particular. It is meant as an overview of the various methods that have been applied in the field and a quick introduction into how computational gene finder are built in general. A beginner to the fiel could use this book as a guide through to the main points to think about when constructing a gene finde , and the main algorithms that are in use. On the other hand, the more experienced gene finde should be able to use this book as a reference to different methods and to the main components incorporated in these methods. I have focused on the main uses of the covered methods and avoided much of the technical details and general extensions of the models. In exchange I have tried to supply references to more detailed accounts of the different research areas touched upon.
The book, however, makes no claim on being comprehensive. As the amount of available data has exploded, as has the literature around computational biology and comparative genomics over the past few years, and although I have attempted to leave no threads untouched, it has been impossible to include all different approaches and aspects of the field Moreover, I am likely to have missed several important references that rightfully should have been mentioned in this text. To all of you I sincerely apologize.Single Species Gene Finding
Sequence Alignment
Comparative Gene Finding
Gene Structure Submodels
Parameter Training
Implementation of a Comparative Gene Finder