Coloring methods in Multiple Alignment View
Introduction
This tutorial will serve as a consolidation space for all existing help on Coloring methods in Multiple Sequence Alignment View.
Step 1: Download example file
Download example file
Step 2: Open Multiple Sequence View
Open the example file (Open - File Import). Set the File Format drop-down to "Text Alignment files".
Click Next twice, then Finish, leaving the default settings. New project will be added to your workspace.
Right-click the new project and select Open New View command. New View menu will be displayed.
Click on the Multiple Alignment View. Multiple Alignment view will be displayed.
Step 3: Explore Coloring methods
Select your region of interest an zoom to sequence.
Right-click anywhere in your region of interest and select Coloration - Select Method from the context menu.
Alignment Scoring Methods menu will be displayed.
Explore the following available scoring methods (described in detail in the Multiple Sequence Alignment Viewer documentation):
- BLOSUM
- Show Differences
- Frequency-based Difference
- Hydropathy Scale
- Membrane Preference
- Rasmol Amino Acid Colors
- Shapely Amino Acid Colors
- Signal sequence
- Size
- Conservation
Current Version is 3.8.2 (released December 12, 2022)
General
Help
Tutorials
- Basic Operation
- Using Active Objects Inspector
- Configure tracks and track display settings
- Working with Non-Public Data
- Viewing Multiple Alignments and Trees
- Broadcasting
- Genes and Variation
- Generating and Viewing Sequence Overlap Alignment
- Working with BAM Files
- Loading Tabular Data
- Working with VCF Files
- Sequence View Markers
- Opening Projects in Genome Workbench
- Publication quality graphics (PDF/SVG image export)
- Editing in Genome Workbench
- Create Protein Alignments using ProSplign
- GFF-CIGAR export for alignments
- Exporting Tree Nodes to CSV
- Generic Table View
- Running BLAST search against custom BLAST databases
- Using Phylogenetic Tree
- Coloring methods in Multiple Alignment View
- Displaying translation discrepancies
- Searching in Genome Workbench
- Graphical View Navigation and Manipulation
- Using the Text View to Review and Edit a Submission
- BAM haplotype filtering
- Displaying new non-NCBI molecules with annotations
- Creating phylogenetic tree from precalculated multiple alignment
- Creating phylogenetic tree starting from search
- Video Tutorials
General use Manuals
- Tree Viewer Formatting
- Tree Viewer Broadcasting
- Genome Workbench Macro
- Query Syntax in Genome Workbench and Tree Viewer
- Multiple Sequence Aligners
- Running Genome Workbench over X Window System
NCBI GenBank Submissions Manuals
- Table of Contents
- Introduction
- Genome Submission Wizard
- Save Submission File
- Reports
- Import
- Sequences
- Add Features
- Add Publication
- Comments
- Editing Tools