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    978-1-43-984117-4
    August 29th 2012

Description

The success of individualized medicine, advanced crops, and new and sustainable energy sources requires thoroughly annotated genomic information and the integration of this information into a coherent model. A thorough overview of this field, Genome Annotation explores automated genome analysis and annotation from its origins to the challenges of next-generation sequencing data analysis.

The book initially takes you through the last 16 years since the sequencing of the first complete microbial genome. It explains how current analysis strategies were developed, including sequencing strategies, statistical models, and early annotation systems. The authors then present visualization techniques for displaying integrated results as well as state-of-the-art annotation tools, including MAGPIE, Ensembl, Bluejay, and Galaxy. They also discuss the pipelines for the analysis and annotation of complex, next-generation DNA sequencing data. Each chapter includes references and pointers to relevant tools.

As very few existing genome annotation pipelines are capable of dealing with the staggering amount of DNA sequence information, new strategies must be developed to accommodate the needs of today’s genome researchers. Covering this topic in detail, Genome Annotation provides you with the foundation and tools to tackle this challenging and evolving area. Suitable for both students new to the field and professionals who deal with genomic information in their work, the book offers two genome annotation systems on an accompanying CD-ROM.

Contents

DNA Sequencing Strategies

The Evolution of DNA Sequencing Technologies

DNA Sequence Assembly Strategies

Next-Generation Sequencing

Sequencing Bias and Error Rates

Coding Sequence Prediction

Introduction

Mapping Messenger RNA (mRNA)

Statistical Models

Cross-Species Methods

Combining Gene Predictions

Splice Variants

Between the Genes

Introduction

Transcription Factors

RNA

Pseudogenes

Other Repeats

Genome-Associated Data

Introduction

Operons

Metagenomics

Individual Genomes

Characterization of Gene Function through Bioinformatics: The Early Days

Overview

Stand-Alone Tools and Tools for the Early Internet

Packages

From FASTA Files to Annotated Genomes

Conclusion

Visualization Techniques and Tools for Genomic Data

Introduction

Visualization of Sequencing Data

Visualization of Multiple Sequence Alignments

Visualization of Hierarchical Structures

Visualization of Gene Expression Data

Functional Annotation

Introduction

Biophysical and Biochemical Feature

Prediction

Protein Domains

Similarity Searches

Pairwise Alignment Methods

Conclusion

Automated Annotation Systems

Introduction

MAGPIE

Generic Model Organism Database (GMOD)

AGeS

Ensembl

Summary

Dynamic Annotation Systems: End-User-Driven Annotation and Visualization

Introduction

Web-Based Genome Annotation Browsers

Stand-Alone Genome Annotation Browsers

Comparative Visualization of Genomes

Web-Based Workflows

Introduction

Principles of Web-Based Workflows

Galaxy

Taverna

Seahawk

Conclusion

Analysis Pipelines for Next-Generation Sequencing Data

Introduction

Genome Sequence Reconstruction

Analysis Pipelines: Case Studies

Next-Generation Genome Browsing

Index

References appear at the end of each chapter.

Author Bio

Jung Soh is a research associate at the University of Calgary. He earned a Ph.D. in computer science from the University at Buffalo, The State University of New York, where he worked at the Center of Excellence for Document Analysis and Recognition (CEDAR). He also worked as a principal research scientist at the Electronics and Telecommunications Research Institute (ETRI) in Daejeon, Korea. His research interests are in bioinformatics, machine learning, and biomedical data visualization.

Paul M.K. Gordon is the bioinformatics support specialist for the Alberta Children’s Hospital Research Institute at the University of Calgary. He has worked at the National Research Council of Canada’s Institute for Information Technology (NRC-IIT) and Institute for Marine Biosciences (NRC-IMB). His current work focuses on developing bioinformatics techniques for personalized medicine.

Christoph W. Sensen is a professor of bioinformatics at the University of Calgary. He has previously worked as a research officer at the National Research Council of Canada’s Institute for Marine Biosciences (NRC-IMB) and as a visiting scientist at the European Molecular Biology Laboratory (EMBL) in Heidelberg. His research interests are in genome research and bioinformatics.

Related Subjects

  1. Bioinformatics

Name: Genome Annotation (Hardback)Chapman and Hall/CRC 
Description: By Jung Soh, Paul M.K. Gordon, Christoph W. Sensen. The success of individualized medicine, advanced crops, and new and sustainable energy sources requires thoroughly annotated genomic information and the integration of this information into a coherent model. A thorough overview of this field, Genome...
Categories: Bioinformatics