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Wrapping Up Artemis Practice

In this screencast we repeat the hands on practice for Artemis.
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Hello everyone, my name is Dr. Anna Protasio In this Screen Cast, we are going to go through the same steps as you have done so far in the exercise of more ‘Practice with Artemis’. As a first step, we are going to open the DNA and annotation files of S. typhi. I have my Artemis Window open here. I’m going to go to File, Open [my] File Manager, and I’m going to navigate to the location where the files are. In this location, S.typhi DNA already appears in my navigation. So I can double click, and voila [here], the genome of Salmonella typhi is represented in Artemis. Notice that it looks naked. There are no annotations in this Artemis Window.
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And that is because the annotation for this particular file is - for this particular genome - is in a different file. In order to load the annotation, I’ll go to File- Read An Entry, and I can select the annotation, which in this case is S. typhi .tab. Remember that the annotation can come in different formats. It could have been .embl or the extension can vary.
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It says that it’s reading from this File. It’s also asking me whether I want to see the warnings. I’m going to say No. And here is the annotation. You can see the different CDSs [CoDing Sequences] in different colours. And as I click on the different genes, then they get highlighted. And you can also [see] it also highlights in the Annotation Panel here at the bottom. Remember that if we double click on one particular feature of CDS [a CoDing Sequence], then all the windows are going to be centred on that particular CDS [CoDing Sequence].
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Our next task is to navigate to one of the genes called fbaB. In order to do this, I am going to use the navigation window. Go to Navigator, and go to Feature with Gene Name fbaB.
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We can’t see it here, but if I move the Window, that’s the gene over there. I’m going to close this. So this is the fbaB gene.
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The next thing we’re going to learn is to visualise the nucleotides and amino acid sequence of this gene in a separate Window. To do that, I can go to View. Bases - Bases of Selection. And in this case, I want to see them As FAST or FASTA. If I click here, these are the nucleotides that are composing the fbaB gene.
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From this window, we can copy and paste by highlighting, and then put it - in another - in another File if we want, or in a Blast search if need be. Notice that you can save this to a File. I’m not going to do that right now. We can also visualise the amino acid sequence,
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either going through the same process: View- Amino Acids- and Amino Acid Selection of FASTA. Or we can also access the same menu by doing double click on the feature, going to View- Amino Acids- Amino Acids Of Selection As FASTA. So notice that these Menus reproduces the one that is on the top banner. And here opens a new Window, where we can see the amino acid sequence of the File- of the protein fbaB.
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If we wanted to Save this sequence to a File, we can either do it as I showed before or we can go with a highlighted feature, go to File- Write- [Write] - Bases Of Selection- as FASTA [format] or EMBL [format] or Genbank format. I want to choose EMBL format. So here I can just say S. Typhi fbaB gene, and I am going to put the extension .embl So I remember that I saved this as an .embl File.
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I can then navigate to that location and open the File if I want to. You can also save more than one at the same time by selecting for features, for example, File- Write Bases Of Selection as FASTA this time, 4genes_ fbaB.
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fasta. And there it is the saved File.
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And then select Feature Plots. This opens a Window in which we can see the Hydrophobicity of the protein encoding that particular gene, the Hydrophilicity of the protein encoding the gene, and the Coiled-Coil regions, or the probability of encountering a Coiled-Coil region. Look at this slider on the side. Works the same as for the GC [Guanine-Cytosine] content that we’ve seen before. We can smoothen the Plot or make it sharper. I notice that the Hydrophobicity is right opposite to the Hydrophilicity. And they look like mirrors, because where a protein is going to be very Hydrophobic, it’s going to be NOT Hydrophilic. Now, to the Coiled-Coil regions.
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Coiled-Coil regions, as we explained earlier, are regions of highly structural regions in the protein and they can take part in very important functions. What this block is showing us is the probability of finding a Coiled-Coil region along the length of the amino acids of that protein. So here, where we can see, that’s the towards the amino acid 120 towards the end of the protein. There seems to be an increased probability of encountering a Coiled-Coil region. Therefore, we can have a little bit more insight into what these proteins might be doing.
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This is the end of the Screen Cast. I hope you have enjoyed it and I hope you are now a bit more fluent in Artemis.

In this screencast we demonstrate the previous exercise step by step.

You will review how to open a DNA file and load its annotation. You will also learn how to save nucleotide and amino acid sequences from individual and groups of CDS to files. Then, we will explore some predicted protein characteristics that can be displayed using Artemis.

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Bacterial Genomes II: Accessing and Analysing Microbial Genome Data Using Artemis

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