Function Menu
License Activation
Function Overviews and Basic Operation
Work Bench
Feature Map- Feature Key and Feature
Management and Operations of Feature Keys- Attributes of Feature Keys
- IMC Original Set Feature Keys
- Types and Roles of Qualifiers
- IMC Original Set Qualifiers
- View and Edit Qualifiers
- Feature Position on Genome Sequence
- Feature Fragmentation
- Feature Synthesis
- Feature Fusion
- Feature Operators
- Link and Refer on Feature
- Feature Mapping
- Register, Edit, Delete Feature
- Feature Appearance
- Join and Delete Position
- Feature Categorization and Presentation
- Import Feature
- Export Feature
- Numbering of Feature
Sequence and Data Input and Output- Genome / Sequence Viewer / Editor
GenBank EMBL Viewer
Sequence Viewer
Annotation Viewer- Multiple Genome Viewer (Linear Map)
Circular Genome Viewer-Designer
Plasmid Map Viewer-Designer
Trace Viewer - Editor- Labeling and Coloring
- Description Window
- Amino Acid Sequence Profile Viewer
- Multiple Alignment Viewer
Phylogenetic Tree Viewer- GT Alignment Viewer
- Restriction Enzyme Map Window
Search Sequence and Annotation- Cloning
- Sequencing
- Gene and Genome Sequence Analysis
- Genome Annotation
Genome Comparison- Multiple Aligment
- Phylogenetic Tree
- Multiple Linear Genome Map
- Gene Cluster Alignment
Multiple Circular Genome Map
Dot Plot Analysis
Venn Diagram Analysis- Core Genome Analysis
- Global Genome Rearrangement Analysis
- Local Genome Rearrangement Analysis
- Mutation Analysis
- Enzyme Alignment by EC Number
- Unique Region Analysis
- Genome Mapping
- Expression Analysis
- Metabolome Analysis
- Genome Design
Settings- Tools
- Window and Dialog Description
- What is "Do It Yourself" Genome Analysis Software?
- Functions and Operations of GenomeTraveler
Dongle License (HW Key)
IMC Primer
Terminate IMC
Toolbox
Feature Key Search
Keyword Search
Pattern Search
Priming Site Search
Batch Homology Search
Restriction Enzyme
Primer Design
PCR Reaction
Ligation
Gel Electrophoresis
Fragment Modification
DNA Content Analysis
Codon Analysis
ORF Analysis
Database Management
Reverse Complement
Function Overviews and Basic Operation GT Primer GT 11B Practice Velvet Assembly using Training DataGT 11B Practice Velvet Assembly using Training Data
In order to become accustomed to the operation of GT, practice the mechanism and operation of assembly by Velvet using training sample data.
This BAM file is the assembly result of NGS lead by Velvet.
This operation is executable on GenomeTraveler.
Operation
Start GT.
Right-click the Velvet_assembling Node in the TREE pane.
The menu will be displayed.
Select Expand.
The velvet_assembling node is expanded.
Right-click on one Velvet-Assembling node.
The menu will be displayed.
Select Expand.
The node named kmer_21 / velvet_asm.afg is displayed.
Right click on the mouse on that node.
The menu will be displayed.
There is only one menu, select "Convert Afg to Bam".
This is a function to convert the afg format file which is the output file format of Velvet Assembler into the Bam format file which is the viewing file format in the alignment viewer.
A confirmation message will be displayed.
Click "Yes (Y)".
File conversion is executed.
A progress message is displayed during execution.
When finished, a completion message will be displayed.
Click "OK".
The node name is changed to kmer_21 / velvet_asm.bam.
Right-click on this node.
The menu will be displayed.
Select "Show Read Alignment".
A progress message is displayed during display processing.
The Alignment Viewer is displayed.
