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.

The Sequence Databanks as a Prerequisite Tools of the Trade: Data Generation and Data Integration DNA Sequencing Strategies Gene Finding Strategies Database Search Strategies Between the Genes Additional Data Types Emerging Data Single Gene Analysis Tools PCGene: Workstation-based Gene Analysis GCG and EGCG: Server-based Gene Analysis EMBOSS: Today's Reality of Server-based Gene Analysis Static Annotation Systems: Concepts of Data Integration Searching for Evidence: An End-User's Perspective MAGPIE: An HTML-based Genome Analysis and Annotation System Artemis: DNA Sequence Viewer and Annotation Tool Distributed Annotation System (DAS) GMOD Tools Dynamic Annotation Systems: End user-driven Annotation and Visualization Bluejay: An XML-based Genome Visualization and Data Integration System NCBI Map Viewer UCSC Genome Browser Ensemble Genome Browser Gbrowse Other Tools Web Service Based Annotation Pipelines Web Services & BioMOBY Taverna: Workflow Generation by Visual Programming Seahawk: Web Service Integration Coping with Massive Volumes of Data Scalable Representation Level-of-Detail Management Data Visualization 2D Visualization: Represention on a Plane 3D Visualization: Building 3D Models of Genomic Context 4D Visualization: Time-Dependent Data and 3D Models