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Skip to 0 minutes and 5 seconds Today, we have invited Professor Julian Parkhill from the Wellcome Sanger Institute to tell us about Artemis, the software that we use for this course. Hi, Julian, can you tell us how Artemis was born? When I started at Sanger, which was 20 years ago now, we were using a programme called DIANA. And, DIANA simply stood for DIsplay and ANAlyze. And, it was just a simple way of looking at sequence data to integrate the results of a whole bunch of different analyses. When people started generating sequence data many, many years ago in small amounts, then to analyse it, you only had physical printouts.

Skip to 0 minutes and 45 seconds So, you would print out the DNA sequence, and then on top of the DNA sequence and below it, you would print up the six-frame protein translation. And, then you would try and look for the genes, and you’d get a big coloured highlighter, and you’d scroll along, and you’d highlight the genes. And, DIANA was simply a way of doing that in an automated way. It allowed you to mark up where the genes were on the six-frame translation. And, then you could overlay a whole bunch of other analyses. You could look at the codon usage. You could look at the GC content. You could run searches using those. But DIANA was fairly crude.

Skip to 1 minute and 24 seconds And, it was written in some really obscure software that only ran on the Unix workstations we had at the time. So, we wanted to update it, and we wanted to make it portable, and we wanted to make it available as broadly as possible. So, we decided to rewrite it in Java. And, that’s the programme Artemis. And, it was called Artemis simply because DIANA is the Roman goddess of the hunt, and Artemis is the Greek goddess of the hunt. So, you were involved in developing Artemis. But were there are other researchers at Sanger or elsewhere that were also involved? It wasn’t written and then presented to people to use. It was developed by the people who were using it.

Skip to 2 minutes and 6 seconds So, firstly, it grew out of a system that had been in use for some, and refined for some time. And, then as we started implementing the new version, Artemis, we immediately started using it in our research analysis. So, I was annotating the genome of Campylobacter jejuni at the time. And, I took what was a fairly brave decision to do all of that annotation in this Beta software, this new Artemis, which was not fully functional at the time. But by trying to do the analysis of this new genome in this new piece of software, then it meant that I could work with the programmer to refine it continuously and get it exactly how I wanted it to do that analysis.

Skip to 2 minutes and 53 seconds So, Artemis is what I wanted this programme to do at the time. Do you remember which was the first research paper that you published using Artemis? When we started developing Artemis, it was very much in Beta test mode. It was incomplete and a bit buggy. But we needed somebody to start using it to refine it and work with it. So we just, I had just started annotating the genome of Campylobacter jejuni at the time. And, I made a brave decision to start using this Beta test software on this genome. So, that was the first genome that was annotated, end to end, using Artemis. And, Artemis was really developed whilst we were doing that annotation.

Skip to 3 minutes and 37 seconds We understand that Artemis is widely used. But is there a particular group of researchers that this software is intended for? So, we originally designed Artemis for researchers, for people who were interested in trying to annotate and analyse fairly large pieces of DNA. What we were really surprised and very pleased about was that Artemis gives you a way of visualising genetic information in a really intuitive way. And, it’s become really powerful as a teaching tool.

Skip to 4 minutes and 8 seconds And, we find lots of colleges will just get people to use Artemis to look at sequence because it gives you that intuitive sense of how transcription works, and how translation works, and where all the signals are that you don’t get from just looking at a piece of paper. Thank you, Julian, for your time and for telling us all about Artemis.

The Genesis of Artemis: Professor Julian Parkhill and Dr. Anna Protasio

In this video interview, Professor Julian Parkhill from the Wellcome Sanger Institute shares his experience of the creation of Artemis with Dr. Anna Protasio. Julian talks about the advances in technology that inspired the development of this genome browser, and the first research outputs it facilitated.

In addition to the interview, you can read the ‘open access’ original research paper that accompanied the release of Artemis: Artemis: sequence visualization and annotation. Kim Rutherford, Julian Parkhill, James Crook, Peter Rice, Marie-Adèle Rajandream and Bart Barrell. Bioinformatics, Volume 16, Issue 10, 1 October 2000: 944–945.

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This video is from the free online course:

Bacterial Genomes: Accessing and Analysing Microbial Genome Data

Wellcome Genome Campus Advanced Courses and Scientific Conferences