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.
Biography
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.
