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.

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.

From individual tools to genome analysis, this book provides an overview of annotation strategies and toolkits currently in use. Presenting a combination of principles and practice, the authors elucidate database search engines and HTML-based annotation systems for specialists in computational biology and bioinformatics who use genome annotation in their work. They also introduce web service-based annotation pipelines. The text includes a CD-ROM with MAGPIE and Bluejay, genome annotation systems and viewers that are used in thousands of laboratories around the world.