November 16, 2017   |   Technical note

Looking for a comprehensive database to host and visualise your bacterial genome?

Codon Genomics Genome Database enables you to seamlessly import and visualise your genomes from your cloud storage. Here are step-by-step technical guides that help you to get started with CGBase:

Setup Genome Instance

Step 1. Go to “Applications” -> “CGBASE”.
Step 2. Click on “Configuration” on the upper right corner of CGBASE.
Step 3. Click “New Genome”, enter “Genome Name”, “Description” and select Profile Pictures “Choose File” and click “Add Genome” to setup a genome instance in the CGBASE application.

Add Reference Genome Data to CGBASE

Step 1. Click on “Genomes” drop down next to the “CGBASE” logo, select the genome setup in Step 3.
Step 2. Click on “Genome Data Management” -> “Genome Data”.
Step 3. Click on “Import Genome Data”, enter Descriptions and click “Choose File”.
Step 4. Select Reference Genome in ZIP file format (with a max file size of 10 MB). If the microbial genome has gone through the optimised microbial annotation pipeline, a ZIP format of the genome will be created in the results folder. Click “Import” to import the genome from Arkgene Cloud Storage.
Step 5. The imported genome can be viewed under “Genome Browser” on the left panel.

Add Gene Models to CGBASE

Step 1. Click on “Genomes” drop down next to the “CGBASE” logo, select the genome setup in Step 3.
Step 2. Click on “Genome Data Management” -> “Gene Models”.
Step 3. Click on “Import Gene Models”, enter Descriptions and click “Choose File”.
Step 4. Select gene model in GFF file format (with a max file size of 10 MB). If the microbial genome has gone through the optimised microbial annotation pipeline, a GFF formatted gene model of the genome will be created in the results folder. Click “Import” to import the gene models from Arkgene Cloud Storage (Results Folders).
Step 5. The imported gene model can be viewed under “Genome Browser” on the left panel as additional data track. To view the gene model, check the tick box of the data track on top of the reference genome.

Add Gene Annotation to CGBASE

Step 1. Click on “Genomes” drop down next to the “CGBASE” logo, select the genome setup in Step 3.
Step 2. Click on “Genome Data Management” -> “Annotations”.
Step 3. Click on “Import Annotations”, enter Descriptions and click “Choose File”.
Step 4. Select gene annotation in text file format (with a max file size of 10 MB). If the microbial genome has gone through the optimised microbial annotation pipeline, a text formatted gene annotation of the gene models will be created in the results folder. Select *.annot.txt file and click on “Import” to import the gene models from Arkgene Cloud Storage (Results Folders).
Step 5. The imported annotations can be browsed under “Gene Models” -> Version X (noted that multiple version of Gene Models can imported into CGBase). To search for annotation, the search bar can be used.