Accessing whole bacterial genomes and annotation

Hello, and welcome to this video. My name is Dr. Anna Protasio. I work at the Wellcome Sanger Institute. And today I am going to show you how to access a whole bacterial genome on the internet, download it, and then open it in Artemis. For the first step, we are going to open our internet browser. In this case, Firefox. I should mention that we are working on a Mac in this particular case. I am going to navigate to the NCBI web page, which is www.ncbi and here it appears because we have used it before www.ncbi.nlm.nih.gov, Press Enter. And the genome that we are looking for is going to be the one from Salmonella typhi strain CT18.

We want to access the nucleotide sequence of the genome. So, I’m going to choose Nucleotide from the dropdown menu.

Here we go. In the Search box, I am going to type Salmonella and I think if we just type CT18, that’s going to be enough information for the search engine to find it.

We have a number of entries. Some of them are complete genomes, and some of them are complete chromosomes. I’m going to choose this fifth entry, which corresponds to the complete genome, with an accession number NC_003198.1. But a lot of the other ones will be equivalent. The one above, for example. This takes us to the entry of this particular genome. And we have a lot of information that will help us to identify this particular genome. For example, the Accession Number is very important because this will be different for other submissions of the genome. As well as the Authors who have submitted this particular entry. And the Publications in which this entry has been featured.

If we scroll down, we will start seeing the Features of the genome. And this here is truncated because it’s quite a long one. Imagine all of the genes in the genome will have to be featured in this page. In order to download the file, I will go to the Send to tab at the top right. Click on this. Choose Complete Record - File. And then, I have a choice of the format. Notice that there are various formats. Including FASTA, which will only include the DNA sequence. However, I want to include the annotation as well in this file. So, I’m going to choose GenBank (full). After this, I click on Create File.

And this is going to give me options whether to Open the File or Save the File to my computer. In this case, I’m going to just Save the File, which is going to be downloaded in the Download folders of my computer. To access that file I can use Finder and then go to the Downloads folder. Here it is with a not very unique name, so I’m going to change this name by renaming the File. And I’m going to call it SalmonellaCT18.

I’m going to leave the extension with GB which means GenBank.

Before opening the File in Artemis, I will open it in a Text Editor just so we can see how it looks like. For that I can use TextEdit, which is here in my dock. I’m going to Open a file in my Downloads. And this is how the file looks like. As you can see, it’s very similar to the entry that we have in Firefox.

But this one is not truncated. So after a while if I scroll down, I’ll start seeing the sequences of the proteins that are being encoded in the genome. And if I scroll all the way down, this might be a bit quick, you can also see that the DNA sequence that forms the genome assembly is there. So this file is complete, and we should be able to open it in Artemis. We’re going to test that by opening Artemis.

And we can use the drop down Menu in File, go to the Open File Manager, and from here navigate to the Downloads.

And open the File. This takes a little bit because it’s quite a large File. And it is also common that Artemis will ask me if I want to see the warnings. I’m not interested in that now, so I’m going to say no. And here is the genome of the Salmonella typhi CT18 that we downloaded. You can see the DNA sequence and also the notation.

In this video we’ve shown you how to download a file from the internet containing a whole bacterial genome, how to open it in Artemis, and how to visualise some of these Features. My name is Dr. Anna Protasio, and I encourage you to leave your thoughts and comments in the comments area. Thank you very much.