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