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Overview

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

The Download Area

Gene Search

1. Specifying a gene search

2. Analyzing search results

3. Saving search results

4. Access to Portal 5.0 Search tools

Search "Classic" (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

Alignment Search (using BLAST and other programs)

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

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

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

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

Clustering

1. The Clustering Front Page

2. Exploring a Cluster

3. Cluster Phylogenetic Tree Reconstruction

Synteny

Annotation

1. Transcript annotation

2. Functional (protein) Annotation