This book presents a guide to building computational gene finders, and describes the state of the art in computational gene finding methods, with a focus on comparative approaches. Fully updated and expanded, this new edition examines next-generation sequencing (NGS) technology. The book also discusses conditional random fields, enhancing the broad coverage of topics spanning probability theory, statistics, information theory, optimization theory and numerical analysis. Features: introduces the fundamental terms and concepts in the field; discusses algorithms for single-species gene finding, and approaches to pairwise and multiple sequence alignments, then describes how the strengths in both areas can be combined to improve the accuracy of gene finding; explores the gene features most commonly captured by a computational gene model, and explains the basics of parameter training; illustrates how to implement a comparative gene finder; examines NGS techniques and how to build a genome annotation pipeline.

This book presents a guide to building computational gene finders, and describes the state of the art in computational gene finding methods, with a focus on comparative approaches. Fully updated and expanded, this new edition examines next-generation sequencing (NGS) technology. The book also discusses conditional random fields, enhancing the broad coverage of topics spanning probability theory, statistics, information theory, optimization theory and numerical analysis. Features: introduces the fundamental terms and concepts in the field; discusses algorithms for single-species gene finding, and approaches to pairwise and multiple sequence alignments, then describes how the strengths in both areas can be combined to improve the accuracy of gene finding; explores the gene features most commonly captured by a computational gene model, and explains the basics of parameter training; illustrates how to implement a comparative gene finder; examines NGS techniques and how to build a genome annotation pipeline.

Comparative genomics is a new and emerging ?eld, and with the explosion of ava- able biological sequences the requests for faster, more ef?cient 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 ?nding in general and of comparative approaches in particular. It is meant as an overview of the various methods that have been applied in the ?eld, and a quick introduction into how computational gene ?nders are built in general. A beginner to the ?eld could use this book as a guide through to the main points to think about when constructing a gene ?nder, and the main algorithms that are in use. On the other hand, the more experienced gene ?nder 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.