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
Genome Comparison Gene Cluster Alignment IMC O10A Operation of Gene Cluster AlignementIMC O10A Operation of Gene Cluster Alignement
Preparation
Load the closely related genome sequence (CDS must be annotated) to be compared into the current reference directory.
Load one genome into the current main directory.
Operation
Identify the gene of interest (CDS) on the main feature map using keyword search etc.
We will do keyword search here. Select Search -> Keyword Search ... from the menu.
The Keyword Search dialog will be displayed.
Check the feature key CDS and enter the search keyword (here hisG) in the Keyword (s) text field.
Click "Run".
The Keyword Search Result dialog is displayed.
When you check the list, the CDS will be displayed in the center of the main feature map.
Right-click on the CDS feature searched.
A pull-down menu will be displayed.
Select Show Homology -> Show Homology A.A.
Homology search is executed.
When the search is completed, the Homology Search hit list dialog will be displayed.
Click each line in the dialog.
Each genome of the reference feature map is aligned around homologous CDS.
Right-click on the CDS where the reference feature map lined up.
A pull-down menu will be displayed.
Select Gene Cluster Alignment ....
The Gene Cluster Alignment Setting dialog is displayed.
Click "Set".
An execution confirmation message is displayed.
Click "Yes (Y)".
Execution is started and a progress message is displayed during execution.
When execution is completed, the Binary Best Hit (BBH) List dialog box is displayed, and at the same time, bands showing homology are displayed between genomes of related genomes in the reference feature map.
In this state, use the zoom feature of the reference feature map or the scroll button to manipulate the map.
Also, clicking on each line of the BBH List dialog will highlight the homology-related CDS and binding band indicated by that line.
Below is the zoomed out view of the reference feature map.
Below is the click of the line of the BBH list. The part corresponding to the clicked line is highlighted.
Below is the side scroll of the bottom genome.