Visualising genome annotation in Artemis with Martin Aslett

Hello, I’m Martin Aslett, the IT Manager for the Wellcome Genome Campus Advanced Courses and Scientific Conferences team. In this video, we will show you how to view ready-made annotation in Artemis. To do this, we will first need to download an annotation file. I will go to my browser,

go to the Sanger ftp site,

and download the St.tab file.

And then close my browser.

To open this, I firstly will open Artemis.

i’ll then go to the File menu, and open the St.dna file, which you have seen previously.

To load the annotation file, I will go to the File Menu choose “Read An Entry,” and then select the St.tab annotation file and click Open. Click OK. I don’t want to view the warnings, these come up routinely. Click No. You’ll notice there are a lot more details now in all three windows on Artemis.

This includes gene models in various colours and miscellaneous features. In the bottom window, we now have the annotations.

If I double-click on any feature, the window will re-centre on it. There are several primary ways of navigating around Artemis. We can use the horizontal scroll bars or select menu items. These also include the Go To Menu. For example, in the selected feature, I can go to Feature Base Position 75 and this highlights the base within the selected feature. Additionally, one can go to the Navigator via the Go To Menu. So, lets, if you want to go to a particular base, feature with a gene name, feature with a particular qualifier, or various other options. I will go to base 350,000. Again, this highlights the base that I’m looking at.

Another way of navigating is to go to the Select Menu, and you can choose either a Base Range or an Amino Acid Range within a Feature. I will go to a base range and choose base range 2188349 to 2199512. The double full stop is the convention for indicating a range of bases.

You will now notice that the full base range is selected. It is this pink bar, here.

I will scroll through to the end of this base range, and select the gene fbaB.

If I click on it, it becomes highlighted in the bottom panel. I can either double-click on the Feature or just press the E key to open the annotation. You will notice that this gene has an Enzyme Commission number; additional annotations; gene names, including its systematic ID; a note about a similarity to another gene; and the product, fructose -biphosphate aldolase class I. Included in the annotation is a colour. Depending on the genome, the colour is set according to the type of annotation the gene has. If you were editing this gene, you would click Apply after making your edits. Otherwise just click OK to close it. From the View Menu, a number of feature-specific options are available.

For example, I can view the bases of the selected gene in FASTA format.

I will close this.

The View Menu also includes some basic feature plots.

Here we have both a Hydrophobicity plot and a Hydrophilicity plot. The scrollbars can be used to change the window of bases that are included in these plots.

I’ll close this. Additionally, Artemis includes other plots across the whole genome. These are available by the Graph Menu and include a GC content plot.

This is shown here. The vertical scrollbar changes the window for the GC content plot. I am Martin Aslett, and in this video, Ihave shown you some of the basics of searching and navigation of annotation in Artemis. Thank you for watching. Please leave any questions and suggestions in the comments section.