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
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Subcategories
Launch 10
There are the following methods to launch IMC.
- Double click the desktop icon
- Launch from the start menu (Windows)
- Launch from the command prompt (Windows)
- Launch from Terminal (Mac)
Launch IMC 7
There are the following methods to launch IMC.
- Double click the desktop icon
- Launch from the start menu (Windows)
- Launch from the command prompt (Windows)
- Launch from Terminal (Mac)
Launch GT 2
There are the following methods to launch GT.
Double click the desktop icon
Launch from the start menu (Windows)
Launch from the command prompt (Windows)
Launch from Terminal (Mac)
Terminate 5
There are the following ways to terminate IMC.
Normal Termination of IMC
- Select the Exit menu and exit
- Click the "X" button in the main window to exit
- In the case of the above normal termination, the changed various setting parameters are automatically saved.
- Sequences that were being edited in the current sequence directory may be saved automatically, and prompts to save or not may be displayed. You can select this setting in the Feature Setting -> Setup tab pane.
Forced Termination
- Forced termination of IMC (Windows)
- Forced termination of IMC (Mac)
- When forcibly terminating the IMC, the sequences that were in the current sequence directory just before may not be saved. Also, various changed setting parameters may not be saved.
Basic Application Operation 6
The following operations are often used in IMC.
- Load (read) the base sequence file and display the main feature map.
- Perform Keyword Search.
- Find the restriction enzyme recognition site.
- View the sequence from the reverse complement side.
- Perform homology search.
Use IMC for the First Time 0
Please visit when using IMC for the first time.
Use GT for the First Time 5
Please read the following when using GenomeTraveler (GT) for the first time.
Sample data will be installed automatically when GT is started for the first time.
Using this sample data, you can practice the operation.
If sample data is not displayed, confirm the demo directory and change it to the root directory and it will be displayed.
Sample data includes the following.
BAM file import:
Contains the result of importing the BAM file used for assembly and mapping. Each fragment of the BAM file can be viewed with the Alignment Viewer.
Mapping (using LAST):
The reference genomic data and the result of mapping NGS lead using LAST on its genome are stored. You can browse and analyze the reference genome data by activating the IMC, and you can view and analyze the mapping by starting the Alignment Viewer. It is also possible to execute new mapping using the same NGS data.
Assembly (using OASES):
Contains the AFG file of assembly result of NGS lead using OASES. Convert this to a BAM file and start the Alignment Viewer. It is also possible to use the same lead and execute a new assembly.
Mapping (using SLIDESORT):
contains reference genomic data and results mapped using SLIDESORT on its genome. You can browse and analyze the reference genome data by activating the IMC, convert the mapping result to a BAM file, and view and analyze it with the Alignment Viewer. It is also possible to execute new mapping using the same NGS data.
Assembly (using Velvet):
The AFG file of assembly result of NGS lead is stored using Velvet assembler. Convert it to BAM file and start up Alignment Viewer. It is also possible to use the same lead and execute a new assembly.
