Comparative Gene Finding: Models, Algorithms and Implementation

ISBN-13: 9781447168751 / Angielski / Miękka / 2016 / 382 str.

Marina Axelson-Fisk

Opis

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.

Recenzje

"The structure of the book mirrors the learning steps for understanding how to perform gene finding. ... Its target audience is mainly post-graduate researchers or established researchers with a background in mathematics or statistics applied in bioinformatics who need a thorough yet concise overview of this field." (Irina Ioana Mohorianu, zbMATH 1350.92001, 2017)

"It skillfully introduces readers to a difficult subject, while at the same time motivating them to enter this very important area. ... It is best suited for a graduate course or as an introduction for researchers not familiar with this field. ... this is an excellent introduction to comparative gene finding. ... I especially recommend this book to any computer scientist with an interest in current problems in bioinformatics." (Burkhard Englert, Computing Reviews, December, 2015)

Spis treści

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

Blurb

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.