Genome Analysis Software Info Site
Official Technology Information Site of in silico biology, inc.
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 Annotation
Genome annotation is to add an annotation to the genome, more specifically, to describe the attribute (Qualifier) of the feature identified on the genome sequence.
Feature type is classified as Feature Key. The position of Feature is recorded as Position. By the Position on the genome base sequence, the nucleotide sequence occupied by the Feature can be found. In addition, coding region (CDS) translated into amino acid indirectly holds translated amino acid sequence information via Genetic Code Table. It is also important that features such as CDS are identified on either side of the double helix, and it is usually written using the position operator Complement.
Subcategories
Database Management 2
To execute annotation, it is necessary to create a database of nucleic acid sequences or amino acid sequences with annotations added.
IMC has a function to automatically generate a database for Blast search simply by loading the genome sequence.
This function can be used to annotate unknown genomes of closely related species.
A function of generating a large database is also implemented.
The CreateDB function generates a database for local blast search using a file of SuperKingdom that can be downloaded from NCBI and others.
The search database can generate both nucleic acid sequences and amino acid sequences databases.
These files are very large and numerous. When searching, you can join many generated databases and use them as one database name.
It is also possible to build a database on an external server so that it can be searched via the net.
Genome Annotation Tools 0
Tool group for performing genome annotation.
Mainly, the following software are used.
Many software run on Linux, so when using it on Windows, we use an external server etc.
By using Windows emulator, it can also be used in Windows PC local environment.
- CDS identification software
- rRNA identification software
- rRNA identification software
- Motif identification software
- Other
External Annotation Server 0
Since genome annotation processing requires a lot of computation time and often takes a long time, it is widely practiced to execute this on an external server and obtain the result.
In addition, the genetic identification software used for genome annotation is developed to operate on Linux in many cases, it may not be possible to run on Windows.
Even in such a case, there is the merit of installing those software on the external Linux server and annotating it.
Because Mac OS X is based on Linux, many of those identification software work directly in the local environment of the Mac.
However, also in this case manual operation may be delayed when performing manual annotation in parallel, there is a merit of annotating on the external server even on Mac.
IMC has a function to create an annotation database on an external server, and it is easy to generate a search database on the server.
Auto Annotation 1
It is a function to perform genome annotation fully automatically.
When you register a genome base sequence to be annotated, annotation to that genome sequence is performed fully automatically.
You can select the identification software to use before execution and the sequence database to use.
Manual Annotation 1
Manual annotation can be performed using the annotation function installed in the IMC.
IMC has the following annotation tools.
- Annotation Window
- Description Window
- Sequence Viewer
- Sequential number addition function to features
- Unnecessary Feature / Qualifier Removal Function
- Feature operator
- Batch homology search function
- Others
Organization and Submission Tools for Annotation 0
During annotation, we may refer to a lot of information and use special features and qualifiers.
In addition, naming and sequential number addition often become unavoidable in using temporary things in the middle of annotation.
However, when the annotation is over, much of the above information is unnecessary, and submission of annotation may result in errors.
IMC has a function to organize and refine the annotation results when the annotation is over.
The main items are listed below.
- File generation function for DDBJ large base sequence registration
- Sequential number addition function to features
- Annotation db-xref link addition function
- Removal of Feature / Qualifier
- Feature operator
- Other
Add Sequential Number to Features 0
- You can add a serial number to the features narrowed down as a search result.
- Select one of the Qualifiers that each feature has, and a serial number will be added as that value.
- Specifically, it can be operated from each search result screen of feature key search, keyword search, and genome statistical information.
- In addition, a unified serial number can be added to features on multiple selected genome sequences that are on the current main directory.