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