Comparative Gene Finding

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.

Provides detailed descriptions of the models and algorithms and how to implement them Summarizes the advances in the field and gives clear and concise instructions on how to proceed though the project process Updated and expanded new edition, now covering next-generation sequencing technology and conditional random fields Includes supplementary material: sn.pub/extras

Klappentext

This unique text/reference presents a concise guide to building computational gene finders, and describes the state of the art in computational gene finding methods, with a particular focus on comparative approaches. Fully updated and expanded, this new edition examines next-generation sequencing (NGS) technology, including annotation pipelines for NGS data. The book also discusses conditional random fields, enhancing the broad coverage of topics spanning probability theory, statistics, information theory, optimization theory, and numerical analysis.

Topics and features:

• Introduces the fundamental terms and concepts in the field, and provides an historical overview of algorithm development
• 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, reviewing the different steps and accuracy assessment measures used to debug and benchmark the software

• Examines NGS techniques, and how to build a genome annotation pipeline, discussing sequence assembly, de novo repeat masking, and gene prediction (NEW) Postgraduate students, and researchers wishing to enter the field quickly, will find this accessible text a valuable source of insights and examples. A suggested course outline for instructors is provided in the preface. Dr. Marina Axelson-Fisk is an Associate Professor at the Department of Mathematical Sciences of Chalmers University of Technology, Gothenburg, Sweden.

  Inhalt

Introduction.- Single Species Gene Finding.- Sequence Alignment.- Comparative Gene Finding.- Gene Structure Submodels.- Parameter Training.- Implementation of a Comparative Gene Finder.- Annotation Pipelines for Next Generation Sequencing Projects.