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This content is taken from the Wellcome Genome Campus Advanced Courses and Scientific Conferences's online course, Bacterial Genomes: Antimicrobial Resistance in Bacterial Pathogens. Join the course to learn more.

Skip to 0 minutes and 6 seconds Hello. My name is Dr. Ulrike Böhme. I am a scientist working at the Wellcome Sanger Institute. In this short demonstration, we will show you how to download ACT. You will learn how to install the tool on a Mac. In a previous course called Bacterial Genomes – Accessing and Analysing Microbial Genome Data, we showed you how to download Artemis. When you download Artemis, you download a package with several programmes. This package also includes ACT so there is a possibility that you already have ACT on your computer. If not, we will now show you how to download and install it on a Mac. I’m going to navigate to the ACT page.

Skip to 0 minutes and 46 seconds The easiest way to do this is to type in Google “ACT,” or just open your web browser and then search for “ACT” and “Sanger”.

Skip to 1 minute and 1 second The very first hit is the correct hit, we want to download and install the tool. Let’s go to the GitHub page. GitHub is a repository for scientific software.

Skip to 1 minute and 19 seconds Let’s scroll down to see Software Availability. There are different options, it depends on which operating system you use. You have to download it. We are going to download the Mac OS version. Please note that there is a second option for CHADO. This is a database, so we are not going to cover this in this course. We will download here this version. Also, please note, for this version– for this newest version of ACT, you need Java 11. You have to download it beforehand. If you cannot download that or install it, you have to go to this Artemis FTP site to download ACT, a previous version. Let’s click on the Mac version.

Skip to 2 minutes and 5 seconds This is now downloading, it may take a few seconds. Once this is done, I go to the Downloads folder.

Skip to 2 minutes and 17 seconds And you can see here in the Downloads folder, we have now a file called dot dmg. We double-click on that file-, and–

Skip to 2 minutes and 30 seconds this takes a few seconds – and now you can see something you’ve already seen in the previous course where we’ve installed Artemis. And as you can see, ACT is part of a package with different programmes. We are not going to cover BamView and Circular- Plot, we’re now interested in ACT. To install it, you can either use it from here, from this tool section, or you can move this in your Application folder or you can move it on the desktop, and this is what I’m going to do now. So just move ACT onto the desktop and here now you can see the nice ACT logo. Double-click on that.

Skip to 3 minutes and 14 seconds Macs often have a security issue with ACT in that it comes from an unidentified developer. To fix this, we just have to go to the System Preferences. I will do so now.

Skip to 3 minutes and 31 seconds We have to go to Security and Privacy. And you can see here ACT was blocked because it is not from an identified developer. Let’s just click on here Open Anyway.

Skip to 3 minutes and 54 seconds OK. So now, to open ACT, you just need to double-click on the ACT icon, and it will set a working directory. I would like to have everything saved on the desktop. You just need to browse, choose desktop. Just choose Desktop and then say OK. And here it is. You’ve got ACT installed now on your computer. In this video, we have shown you how to install Act on a Mac. Thank you for viewing. Please leave your suggestions and questions in the comments area.

Using Artemis Comparison Tool (ACT) to browse a XDR Typhoid genome Part 1

In the step to follow, we will use ACT to analyse a representative Salmonella Typhi genome (labelled as BL0006) of the extensively drug resistant (XDR) Typhoid outbreak you have been investigating

We are going to use a genome browser and genome comparison tool called Artemis Comparison Tool (ACT). ACT was developed at the Wellcome Sanger Institute and is freely available to download for PCs and Mac.

You will need to download the Artemis Comparison Tool (ACT). Watch this installation video to download and open ACT on your computer, before proceeding to the next step. Instructions on ACT are also available via this website (https://www.sanger.ac.uk/tool/artemis-comparison-tool-act/).

Data files download

You will also need to download the four files below (Important - in order to download data from the Sanger ftp site, you will need to copy and paste the link in your internet browser, rather than just click on it. We recommend use of Chrome or Firefox browsers for downloading data files):

  • BL60006.dna

ftp://ftp.sanger.ac.uk/pub/resources/coursesandconferences/Online_Courses/AMR/BL60006.dna DNA sequence of a representative XDR Salmonella Typhi genome.

  • Salmonella_enterica_subsp_enterica_serovar_Typhi_str_BL60006_v1.1.gff

ftp://ftp.sanger.ac.uk/pub/resources/coursesandconferences/Online_Courses/AMR/Salmonella_enterica_subsp_enterica_serovar_Typhi_str_BL60006_v1.1.gff genome annotation of BL60006.

  • CT18.gbk.txt

ftp://ftp.sanger.ac.uk/pub/resources/coursesandconferences/Online_Courses/AMR/CT18.gbk.txt DNA sequence and annotation of a Salmonella typhi reference genome.

  • CT18_vs_BL60006_blast.result.txt

ftp://ftp.sanger.ac.uk/pub/resources/coursesandconferences/Online_Courses/AMR/CT18_vs_BL60006_blast.result.txt result of blasting CT18 against BL60006.

You are now ready to browse the XDR Typhoid genome, so let’s proceed to the next step.

Installation video by courtesy of Ulrike Böhme, researcher in parasitology at the Wellcome Sanger Institute

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This video is from the free online course:

Bacterial Genomes: Antimicrobial Resistance in Bacterial Pathogens

Wellcome Genome Campus Advanced Courses and Scientific Conferences