Analysing viral genomes in Artemis
Before we finish week 2 let’s recap the steps you need to take to download a genome from a public repository and open the genome in Artemis.
With Artemis you can not only view and analyse bacterial genomes but also viral genomes and small eukaryotic genomes.
For this exercise we will take a break from bacterial genomes and look at a viral genome, the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) genome. This is the virus that causes coronavirus disease 2019 (COVID-19), the disease that led to a global pandemic.
First you need to download the viral genome. We will look at the first sample of SARS-CoV-2 that was sequenced. Here is the link to the GenBank record: https://www.ncbi.nlm.nih.gov/nuccore/MN908947/
To download the GenBank file, go to Send to on the right-hand side of the GenBank record, choose Complete Record, destination File and as format choose GenBank (full). Then click on Create File. The name of the file that you downloaded from GenBank is called sequence.gb. Let’s rename the file and give it a more meaningful name, e.g. SARSCoV2.gb. This file contains the sequence and annotation.
Let’s open Artemis and choose the file called: SARSCoV2.gb
Once you’ve opened Artemis you should get a view like this. To view the complete genome use the slider (marked with a red circle) on the right-hand side to zoom out.
How many genes can you find on this genome (also called CDSs)?
Can you find out the gene products? (Hint: Choose Edit and then Selected Features in Editor or press E on your keyboard).
Alternatively, with a right click in the Feature menu, there are additional options to choose from. Choose Show Products. Now you can see all the products in the Feature menu.
What is the size of the genome? (Hint: Go to View on the top panel and select Overview). Can you also find other useful information in the Overview section?
What could you do to get additional information about the genes? Discuss with your fellow learners.
We hope you found the quick detour to viral genomes interesting. Let’s go back to the bacterial genome exercises where you will learn many more useful Artemis features!
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