Overview
Simple Search
1. Searching for Gene Model Hits to Multiple Databases
1.1. Results from Searches for Hits to Multiple Databases
2. Searching for Gene Model Hits to InterPro
2.1. Results from Searches for Hits to InterPro
3. Searching Tracks
4. Searching Gene Models Directly
Advanced Search
1. Search Basics
2. Searching Directly Against Annotations
3. Searching by Homology
4. Searching in Previous Search Results
5. Searching Specific Fields
6. Downloading Sequences
Alignment Search (using BLAST and other programs)
1. Running Alignment Search
2. Viewing Graphical Alignment Results
2.1. Viewing Information About the Alignment Search
2.2. Zooming and Navigating
2.3. Working with Hit Results
3. Viewing Raw Alignment Results
The Genome Browser
1. What is a Scaffold?
2. The Genome Viewer
2.1. Alignment Details
2.1.1. Alignment Summary Table
2.1.2. Alignment Graphic Display
2.1.3. Alignment Hit Reports
2.2. The Protein Page
2.2.1. Protein Summary Information
2.2.2. Ontology, InterPro, and Annotation Information
2.2.3. Links to Alternative Views
2.2.4. Transmembrane Domain Graphs
2.2.5. Protein Hit Tracks
2.2.6. Gene Sequence Viewer
2.2.7. Protein Alignment Tracks
2.2.8. Protein Alignment Reports
2.2.9. The Flipped View of a Protein Page
2.2.10. Viewing Amino Acid Sequences
2.2.11. Customizing the Protein Page Display
2.3. Scaffold Info
2.4. Scaffold Sequence Viewer
2.5. Repeat Sequence Viewer
2.6. The Track Editor
3. Browser Navigation Controls
4. The Browser Tool Bar
4.1. Tool Bar Browser Controls
4.2. Tool Bar Track Controls
4.3. Saved Views
The GO Browser
1. Browsing through Terms and Gene Products
2. Searching GO
3. Viewing Gene Products
The KEGG Browser
1. Searching in KEGG
1.1. Using KEGG Search Results
2. Browsing through Pathways
3. Viewing Enzymes Related to a Pathway
4. Viewing Predicted Genes Related to a Pathway
5. Viewing Maps of Reference Pathways
The KOG Browser
1. Browsing through Classifications and KOGs
2. Searching for KOG IDs or Descriptions
3. Viewing Lists of Predicted Genes