1. The Portal Front Page 1.1 Genome Search 2. Organism Portals 3. "Organism Group" Portals 4. Logging in and Registering as an annotator 5. The myPortal Page 5.1 Managing your Custom Tracks 5.2 Saved Alignment Search Results
1.1 Genome Search
5.1 Managing your Custom Tracks 5.2 Saved Alignment Search Results
1. Download page with web UI 1.1 Downloading IMG annotation Data 2. Download with Globus service 3. Download with API
1.1 Downloading IMG annotation Data
1. Specifying a gene search 2. Analyzing search results 3. Saving search results 4. Access to Portal 5.0 Search tools
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 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
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 3. Searching Tracks 4. Searching Gene Models Directly
1.1. Results from Searches for Hits to Multiple Databases
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
1. Running an Alignment Search 1.1 Specifing the Query 1.2 Setting Search Criteria 1.3 Setting Alignment Parameters 1.4 Choosing Target Genomes 2. Viewing Alignment Results 2.1 Monitoring the Progress of Your Job 2.2 Exploring the Alignment Hit Table 2.3 Exploring Alignment Hit Graphs 2.4 Analyzing Individual Hits in Detail
1.1 Specifing the Query 1.2 Setting Search Criteria 1.3 Setting Alignment Parameters 1.4 Choosing Target Genomes
2.1 Monitoring the Progress of Your Job 2.2 Exploring the Alignment Hit Table 2.3 Exploring Alignment Hit Graphs 2.4 Analyzing Individual Hits in Detail
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 2.7. Uploading and Sharing Custom Tracks 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
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 2.7. Uploading and Sharing Custom Tracks
2.1.1. Alignment Summary Table 2.1.2. Alignment Graphic Display 2.1.3. Alignment Hit Reports
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
4.1. Tool Bar Browser Controls 4.2. Tool Bar Track Controls 4.3. Saved Views
1. Browsing through Terms and Gene Products 2. Searching GO 3. Viewing Gene Products
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
1.1. Using KEGG Search Results
1. Browsing through Classifications and KOGs 2. Searching for KOG IDs or Descriptions 3. Viewing Lists of Predicted Genes
1. The Clustering Front Page 2. Exploring a Cluster 3. Cluster Phylogenetic Tree Reconstruction
1. Transcript annotation 2. Functional (protein) Annotation
