Comparative Gene Finding

Models, Algorithms and Implementation
2. Auflage 2015
ISBN: 978-1-4471-6692-4
Verlag: Springer

Buch, Englisch, Band 20, 382 Seiten, Format (B × H): 160 mm x 241 mm, Gewicht: 7273 g

Reihe: Computational Biology

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.

Zielgruppe

Research

Autoren/Hrsg.

Axelson-Fisk, Marina

Fachgebiete

• Naturwissenschaften Biowissenschaften Angewandte Biologie Bioinformatik
• Mathematik | Informatik EDV | Informatik Angewandte Informatik Bioinformatik
• Naturwissenschaften Biowissenschaften Biowissenschaften Genetik und Genomik (nichtmedizinisch)

Inhaltsverzeichnis

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