Genome Annotation: 1st Edition (Hardback) book cover

Genome Annotation

1st Edition

By Jung Soh, Paul M.K. Gordon, Christoph W. Sensen

Chapman and Hall/CRC

270 pages | 20 Color Illus. | 62 B/W Illus.

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Hardback: 9781439841174
pub: 2012-08-30
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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.

Table of 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


Mapping Messenger RNA (mRNA)

Statistical Models

Cross-Species Methods

Combining Gene Predictions

Splice Variants

Between the Genes


Transcription Factors



Other Repeats

Genome-Associated Data




Individual Genomes

Characterization of Gene Function through Bioinformatics: The Early Days


Stand-Alone Tools and Tools for the Early Internet


From FASTA Files to Annotated Genomes


Visualization Techniques and Tools for Genomic Data


Visualization of Sequencing Data

Visualization of Multiple Sequence Alignments

Visualization of Hierarchical Structures

Visualization of Gene Expression Data

Functional Annotation


Biophysical and Biochemical Feature


Protein Domains

Similarity Searches

Pairwise Alignment Methods


Automated Annotation Systems



Generic Model Organism Database (GMOD)




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


Web-Based Genome Annotation Browsers

Stand-Alone Genome Annotation Browsers

Comparative Visualization of Genomes

Web-Based Workflows


Principles of Web-Based Workflows





Analysis Pipelines for Next-Generation Sequencing Data


Genome Sequence Reconstruction

Analysis Pipelines: Case Studies

Next-Generation Genome Browsing


References appear at the end of each chapter.

About the Authors

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.

About the Series

Chapman & Hall/CRC Computational Biology Series

This series aims to capture new developments in computational biology, as well as high-quality work summarizing or contributing to more established topics. Publishing a broad range of reference works, textbooks, and handbooks, the series is designed to appeal to students, researchers, and professionals in all areas of computational biology, including genomics, proteomics, and cancer computational biology, as well as interdisciplinary researchers involved in associated fields, such as bioinformatics and systems biology.

For more information or to submit a book proposal, please contact <a href="[email protected]">Elliott Morsia</a> ([email protected]).

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BISAC Subject Codes/Headings:
COMPUTERS / Programming / Games
SCIENCE / Life Sciences / Biology / General
SCIENCE / Biotechnology