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Computer based practicals

Computer based practicals for genomics
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Hi. I’m Fran Gale. I’m the head of Science Engagement and Enrichment for Wellcome Connecting Science, and I’m going to tell you a little bit about our website, yourgenome.org. Now, this is a learning resource all about DNA genes and genomes, and we’ve got a whole range of articles on there, short reads, long reads, and also case studies, so something for everyone, depending on your reading ability. Now, we also have an activities and resource section, and this has got a range of different resources from videos and animations, but also some classroom-based activities. Now, these can be paper-based, or they can be computer-based, and we have some that are a little mixture of both.
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So one activity, Function Finders, is all about the central dogma, so DNA to protein. And this is an activity that you can do with probably students age 14-plus. So it consists of a few elements. So I’m going to talk about the paper-based version first. So there is a worksheet, which looks like this, and you’ve got a codon wheel, which looks like this. And then you have a booklet of profiles. Now, you don’t have to print these things out. All of these can be accessible as a PDF on a computer as well. The first step in the process is to translate a DNA sequence into an amino acid sequence.
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So you can see here, the amino acid sequence is made of different codons, about 12 of them. So let’s take the first one. The first codon is ATG. So use your codon wheel. You start from the middle and you go A, T, G. Work your way out, and that goes to what the amino acid letter is going to be. In this case, it’s M. So let’s try the second one. It’s A, A, G. So you will go A, A, G. That gives you a K. So your students just work through the code using the codon wheel, and then they’ll come out with a sequence of about 12 amino acid letters.
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Now, this isn’t going to spell out a word, but what we are going to do is take that code, and we’re going to look in our booklet and see, well, can we find a matching protein? So this one started M, K, and then the next letter is S. You look through it, and then you find it. And in this case, this one– and it’s a antifreeze protein which is found in an Atlantic wolffish. So this protein profile will tell you what the protein is, even what it looks like, and what species it’s found in.
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So far I’ve shown you just a purely paper-based version of this, but we do have a second version called Function Finders BLAST, and this is a computer-based version. So you carry out the paper elements of it, so you translate your DNA sequence into an amino acid sequence. But rather than looking on a paper profile for your protein, you actually go into a real scientific database called UniProt. So I’m going to walk you through the steps on how you do this. The first step is to type in uniprot.org/blast into your browser. Then you’ll come up with this screen here. Now, you’ll see in the box there that you can enter a nucleotide sequence.
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So what we’re going to do is just type in the letters of our sequence. So in this case, we could use M, K, S, A, I, L, T, G, L, L, F, V. And then you press the BLAST button. And this may take a minute or so, but then you’ll soon get a sequence of record hits. And what this BLAST search is doing is comparing your sequence with hundreds of thousands of other protein sequences in this database and finding the best matches. And it’ll even give you a probability number, an e value, of how similar it is to those records that it’s matching against.
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So once you’ve got your hits– that’s what we call them, the hits– you can then philtre them by going down the left-hand side and clicking just Reviewed. And this means that these have been curated by people rather than just algorithms. Then you can find the best e match, which is generally the top function. You’ll see it’s 100% match or similar. And then you click on this. And what you’ll then find is you get a record of what the protein is, what species it is, and what the function of that protein is. So that is the computer-based version. So how does this relate to the real world?
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Well, the database that we’ll use in this activity is curated and used by hundreds of scientists all around the world. It’s a global scientific resource. So your students are, by doing a BLAST search using UniProt, are actually doing day-to-day things that scientists are doing in their everyday jobs. So to give you an example of how BLAST can be used, a good example is imagine a gene has been identified in a mouse that they don’t know what the function is. They can then BLAST that gene against other genomes, a human genome. Could be other rodents, could be other animals, and they can then identify, is that gene present in those genomes, and what does that gene actually do?
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So that is a really good example of how BLAST is used, and your students are carrying out a very similar role. So hopefully you’ve now got a taste of what Function Finders is and how to use the paper-based version as well as the BLAST version. And I really wanted to hear how you get on with your students. So if you have a go at it or have got recommendations for other bioinformatics activities, please do let us know in the discussion section.

We might not all have the budget or capacity to do highly involved lab experiments in the classroom, but there’s other areas of genomics that don’t require this type of kit.

Bioinformatics is a rapidly growing area of biology and genomics that centres around data and computational skills, to inform and understand data from experimental research. This lends itself to running bioinformatics based activities in the classroom, which might be much more accessible to many classrooms than experimental activities – some of them don’t even require student computer access!

In the video, we introduce one of our favourite bioinformatics based activities – Function Finders – which can be flexibly delivered as a paper-based or computer-based activity. We’ve also linked some other great computer-based activities below.

Have you tried any bioinformatics or computer based activities with your students? Let us know your favourite activities in the discussion area.

Links:

Function Finders Activities (yourgenome.org): paper based activity to introduce the central dogma

Function Finders BLAST (yourgenome.org): computer based activity to introduce bioinformatics

You vs. Machine (yourgenome.org): interactive highlighting the speed of sequencing

Data Explorer (HHMI): Online activity where students can explore data visualisation

Explore Epigenetics (Webpage): A series of activities around the topic of epigenetics

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