Genome annotation /

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.