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Viewing your first DNA sequence in Artemis

Opening a FASTA file in Artemis and showing some of the basic functionality, including the navigation tools.
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Hello, I am Pablo Tsukayama, and I am a visiting researcher at the Wellcome Sanger Institute. In this video, I will show you how to open and visualise a sequence file using Artemis on a Mac. Artemis is a free DNA viewer and annotation tool developed at the Wellcome Sanger Institute. It allows the visualisation of various file types, from simple sequence files to annotation entries, as well as various analyses in an intuitive graphical format. It is routinely used by the pathogen genomics group at the Wellcome Sanger Institute and various other groups around the world, for annotation and analysis of both prokaryotic and eukaryotic genomes.
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The aim of this video is for you to become familiar with the basic functions of Artemis using a reference Salmonella typhi genome. There are many, many more functions that are specific to genetic analysis, and we encourage you to explore some of these on your own. By now, you will have downloaded the Artemis software, which is available online for free. And your reference Salmonella genome sequence, which we’ll show you in a little bit. So, first, we will go to Mozilla Firefox to download our file, and we will type in the directory that we are listing below. You will download it from an FTP site at the Wellcome Sanger. Institute.
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Once we’re here, just click right-click on the St.dna file and Save it to your desktop.
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Now, we’ll go ahead and double-click on the Artemis software, and it will ask you to select a working directory to save temporary files for this session. So, now we will select the desktop and if you click in this box, it will record this location for next time and will not prompt you to enter it again.
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Once Artemis is open, we’ll go to File, Open, and select the sequence we just downloaded.
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So, here it is, basic Artemis window. The first thing you will see are these three panels, which display different levels of information of your genome sequences. But for now, let’s focus on the top and middle panels. Both of these actually show the same information, but the middle panel is a zoomed-in version of the top panel. So, if you go to the right-hand side and move the scroll bar, you can see different levels of zoom-in. And you can go half the way from base zero to the very end of your bacterial chromosome. And that’s around 4.8 million base pairs. In the middle section, for each amino acid, you will see the corresponding codon.
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So, this is displaying the forward and reverse strands in their three reading frames. And for each reading frame you will see an amino acid and its corresponding codon.
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And you will see if I highlight a section of the reading frame here, it also highlights it on the top section. If you double-click any specific feature on your panels, it will centre it on your Artemis window. Now let’s zoom out for a little bit and you start noticing these vertical lines in both panels. Each of these black vertical lines represent the stop codon on each coding frame. You will notice that they are not evenly represented in the genome. So, here’s a question for you. What do you think are these long stretches of DNA that do not have stop codon in there? It is likely that they are open reading frames that encode for specific proteins.
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And we will confirm this when we load the annotations in the next section. So, that is how you open and visualise a sequence file using Artemis on a Mac. I’m Pablo Tsukayama. As always, if you have any feedback, please leave it in the comment section below. Thank you for watching.

In this video we will demonstrate how to open a sequence FASTA file in Artemis. We will explore the look of Artemis and some basic tools for navigation.

Before you start with the video, take a moment to download the Salmonella typhi genome sequence in FASTA format from the Wellcome Sanger Institute FTP site. We recommend use of Chrome or Firefox browsers for downloading data files.

ftp://ftp.sanger.ac.uk/pub/resources/coursesandconferences/Online_Courses/Course3/data/S_typhi.dna

You may need to copy and paste the link in your internet browser. This will open the genome sequence itself in your internet browser. To save it to a file, choose the Save As option from your genome browser, and save the file with the name St.dna.

When the video is playing, feel free to follow along on your computer.

Note: Depending on your computer, you may not be able to choose to Open the St.dna file right away from Artemis, as demonstrated in the video. In some cases, you may be required to switch the drop-down menu option of “File type” to ““All file types”. Then, the sequence file St.dna will become available.

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Bacterial Genomes II: Accessing and Analysing Microbial Genome Data Using Artemis

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