Chapter 9. Using EMBOSS under JEMBOSS
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Chapter 9. Using EMBOSS under JEMBOSS
Table of Contents
9.1. Diving In At The Deep End
9.2. Getting Started
9.2.1. Software Requirements
9.2.2. Microsoft Desktop
9.2.3. Apple Macintosh
9.2.4. Unix Platform
9.2.5. Local Installation
9.2.6. Remote Installation
9.2.7.
Jemboss
Session
9.2.8. Session-specific Information
9.2.9. The
Jemboss
Windows
9.2.9.1. Main
Jemboss
Window
9.2.9.2. File Managers
9.2.9.3. Results Managers
9.2.9.4. Text Editors
9.2.10. Settings
9.2.11. Proxies
9.2.12. Servers
9.3. File Management
9.3.1. Local File Management
9.3.2. Home Directory
9.3.3. Working Directory
9.3.4. Move Up a Directory
9.3.5. Creating Data Files in
Jemboss
9.3.5.1. Saving Analysis Results
9.3.5.2. Re-writing a File with New Data
9.3.5.3. Moving a File from a Location on the Desktop Computer
9.3.5.4. Drag and Drop from Remote File Manager
9.3.6. File Manipulation
9.3.7. New Folder Creation
9.3.8. Re-locating Files
9.3.9. Rename
9.3.10. Delete
9.3.11. De-select All
9.3.12. Refresh
9.3.13. Open With
9.3.14. Remote File management
9.3.15. EMBOSS Results
9.3.16. Moving Data between File Managers
9.4. Data Analysis
9.4.1. Programme Selection
9.4.2. Program Categories
9.4.3. Favourites
9.4.4. Alphabetical Program List
9.4.5. Go To Box
9.4.6. Input Section
9.4.6.1. Features
9.4.7. File Input
9.4.7.1. File/Database Entry
9.4.7.2. Browse Files
9.4.7.3. Local Files
9.4.7.4. Remote Files
9.4.7.5. Uniform Sequence Address
9.4.7.6. Paste
9.4.7.7. List of Files
9.4.8. Input Sequence Options
9.4.9. Databases Available
9.4.10. Sequence Format
9.4.11. Begin/End
9.4.12. Reverse Complement
9.4.13. Nucleotide/ Protein
9.4.14. Upper/Lower Case
9.4.15. UFO Features
9.4.16. Load Sequence Attributes
9.4.17. Parameter Selection
9.4.18. Output Section
9.4.19. Output Sequence Options
9.4.20. Sequence Format
9.4.21. Filename Extension
9.4.22. Base File Name
9.4.23. Features Format
9.4.24. Features Filename
9.4.25. Sequence Format
9.4.26. Graphical Format
9.4.27. PNG Graphics
9.4.28. Jemboss Graphics
9.4.29. Graph Options
9.4.30. Main Title
9.4.31. Axis number format
9.4.32. Ticks
9.4.33. Axis Labels
9.4.34. Graph Formatting
9.4.35. Saving
Jemboss
Graphics
9.4.36. Advanced Parameter Selection
9.4.37. Program run options
9.4.38. Interactive
9.4.39. Batch
9.5. Saving Results
9.5.1. Saving locally
9.5.2. Saved Results: Interactive mode
9.5.3. Saved Results: Batch Mode
9.5.4. Saving remotely
9.5.5. Analysis Run Autosave
9.5.6. Local Autosave
9.5.7. Remote Autosave
9.6. Results Retrieval
9.6.1. Retrieving Interactive Results
9.6.2. Retrieving Batch Results
9.6.3.
Job Manager
9.6.4.
Current Sessions Results
9.6.5. Display Results
9.6.6. Delete Results
9.6.7. Refresh Icon
9.6.8. Retrieving Saved Results
9.6.8.1.
Saved Results
Window
9.6.8.2. Local Results
9.6.8.3. Remote Results
9.6.8.4. Results in remote file manager
9.6.8.5.
Results Manager
9.6.8.6. Delete
9.6.8.7. Edit Notes
9.6.8.8. Display
9.7. Customisation
9.7.1. Directory location
9.7.2. Programme Selection
9.7.3. Input/Output Options
9.7.3.1. Sequence Input
9.7.3.2. Adding Sequences
9.7.3.3. Deleting Sequences
9.7.3.4. Parameter behaviour
9.7.3.5. Text Output
9.7.4.
Job Manager
Update frequency
9.7.5. Calculate Dependencies
9.7.6. Proxy and Server Settings
9.8. Utilities
9.8.1.
Jemboss Alignment Editor (JAE)
9.8.1.1. Sequence Manipulation
9.8.1.2. Sequence Manipulation Menu
9.8.1.3. Delete
9.8.1.4. Reverse Complement
9.8.1.5. Trim Sequences
9.8.1.6. Insert Annotation Sequence
9.8.1.7. Display Manipulation
9.8.1.8. Find Pattern
9.8.1.9. Matrix Display
9.8.1.10. Colour Display
9.8.1.11. Colour by Property
9.8.1.12. Colour Identical matches
9.8.1.13. Identity Number
9.8.1.14. Threshold for Positive Matches
9.8.1.15. Data Display
9.8.1.16. Consensus Sequence
9.8.1.17. Consensus Plot
9.8.1.18. Identity Table
9.8.1.19. Sort by ID
9.8.1.20. Save
9.8.1.21. Print
9.8.2.
DNA Editor
9.8.2.1. Data Input
9.8.2.2.
DNA Viewer
9.8.2.3. DNA Wizard
9.8.2.4. DNA Attributes
9.8.2.5. Tick Marks
9.8.2.6. Genetic Features
9.8.2.7. Restriction Enzymes
9.8.2.8. Print
9.8.3. JALVIEW
9.9. Documentation
9.9.1.
Jemboss
User Guide
9.9.2. Application Documentation
9.9.3. Version Number
9.9.4. Tooltips
9.9.4.1. Mouseover Tips
9.9.4.2. Static Tips
9.10. Troubleshooting