Earlier we talked about from using the heat map view, identifying a region of interest, capturing that data from the heat map view, selecting a particular protein and wanting to look at the information for that Jane. Some kind of reiterate some of the things that you can do from the feature page. This is a breadcrumb across the top that describes the genome and then below it describes the gene itself. Jenner, protein and Patric are sort of synonymous terms. This is the identifier in Patric for this particular gene it's 358, so it's saying it's the 358th gene on this particular genome that Rep. See, this is what the gene is known as. The here's the gene symbol for it. This is what we call it, in Patric. This is the protein identifier. It's a hyper link to the resource where you can get that this is the gene identifier. This is what local family belongs to, here's the global family. Then we get into information about the genome, the tax on Ivy for Priscilla Micro D. This is the unique identifier for the genome, which is that number 0.3 and this is what it's called. This is the accession number for cell, actually have two chromosomes. This is the chromosome that this gene is on with it starting in location and its orientation on the string, and so it's going in the forward direction. And generally, this is the way you describe the location of a gene on a genome. The nucleotide length you could get the sequence here. Then you know acid length and the sequence her. We have some different tools that you can go outside of PATRIC to look at. This isn't very exciting chain, so this won't be very interesting, but in other genes you might want to do that. The local family will tell you how many genomes within the genus Persela half this protein. A global family. When you click on this, it would open a new tab, will tell you how many genomes in all of PATRIC have this. The food fam? That's a functional family and it'll tell you how many genomes have that. You can see how many genomes have an identical protein sequence and how many have an identical nucleotide sequence. So by clicking on these like I'll click on this one, I didn't do that in the last time and it'll just show you how many have the identical sequence to it, so not many. And not many of the PATRIC genomes have an identical nucleotide sequence, whereas if you look at the protein sequence, you'll see that 99 of the genomes have an identical protein sequence, or the genes in PATRIC, but only 14 have the same nucleotides, meaning that there are different snip like values for that. So what I wanted to talk to you about today is using the genome browser. Earlier we talked about, here's the gen, it's always in red to draw your eye to it. And here's its gene neighborhood and we talked about the compare region viewer. But remember, when we were at the heat map view and we captured this region. And these are the genes in this region and this is the guy we liked. This is a region that's a genomic Island, Inverse Ella, and so you may want to capture the sequence for not just the gene, but for this region. How would you do that in PATRIC? Well, you would need to go to this path, which is the genome browser, so let's click on this and it's highlighting in yellow, the region of the browser view that corresponds to the gene came into, which is this Jane. Now let me point out that this is one of the few places in PATRIC where you can do direct head-to-head comparisons of the annotations. Every genome in PATRIC is annotated using the RASPK Pipeline, the Refseq annotation it could be pro Kia, or it could be some other annotation pipeline. And each of those have different gene colors, they might have different rules. Annotation pipelines say every gene under 100, base pairs we throw it out. They have different rules for. Jeans overlap how much of an overlap you have between jeans, so there's a lot of under the differences between annotation pipelines, but this is one place that you can see the refseq annotation in the Patrick Annotation. And if you scroll over the ref seq, you can see what the genus called and what it's called him Patrick. This is called a hypothetical protein, as that is, so it's kind of cool thing that where you can actually see that. So let's go back here. And this one started with gene 349 and it ended with gene 365. So I want to go to the genome browser. Wow, this is 360 and 354. Somehow I need to expand this. The password setup on is capturing the sequence that corresponds to this genomic island. So how do I do that? Well, here this is a cool little thing you can do. See this little plus icon here. Let's click on that. And we can include in this table a number of things, including the Stark in the end for that particular gene. And then we need to unclick it, so for this one 349, which is the start of that Genomic Island, and I click on that, 'cause I can't cut and paste anything from this table but once it's highlighted, I can cut and paste from information beyond the green bar. So let's mouse over this and copy it this 344965. Then we go here into the genome browser. My highlight over that and I pasted in. And let's see where it ends. We have to unclick it. This is the last one this 365. And then here's the end sequence. So I copy that and I go here and I paste it. And now we've got the region of the genome that corresponds here to the Genomic Island, and let's click go so you can see now we're getting. There's the 365 and there's the 349. This is shape arouses little particular in this way and that it always is you off of nucleotides, but that's okay, we're close enough here. So how do I download this sequence? The next thing we're going to be doing in Patrick is blasting this data. Let's go here and where it says reference sequence. Let's click on that and then say save track data and then it gives you some options. You can save the highlighted region which would just be that gene. You could save the whole sequence which is 1.2 two megabases. Now we don't want that. Let's do the visible region, okay? And you can either view it or save it. Let's look at it, view it here and see what it looks like, and you can still save it at this point, and so that is how you would find the sequence that corresponds to that particular Genomic Island and Patrick. In the next section of the series, will talk about blasting that data. Thank you for watching and thank you for using Patrick, bye. Hopefully you left that tab open, but if you didn't, we've watched the printing family's order with the unicycle aranca new assemblies and we had to filter the heatmap view so that you could see first we had to incorrect but also filter the heatmap view so you could see the protein families that were present in Unicycler, but missing in some or all of the canoe assemblies. So here's what I want you to do. You now know how to download data from the heatmap and let me just reiterate how awesome that is, often with bioinformatic tools, especially where they have a visualization. You can see the result of the data that you can't grab the actual data that by drawing around that and downloading the data, or being able to open it in a new tab, that's pretty awesome. So draw the box around those proteins from the Unicycler genomes. You can't do it for the canoe, 'cause they're gone from that and then take one of those and go down to the genome browser tab on that feature. So you've drawn the box. You say show proteins, it opens them up, you see the table. You pick one of those. And then you go in and say, I want to see that feature. So you click on that. It's going to open up a new page, so you'll have three tabs at this point. Then, in that, you click on genome browser, and it'll load and show you the genome browser. Click on the gene that we came in on. And first, I want you to get the sequence from the genome browser for that gene. Then, and this is, it's not really hard, you'll be able to figure out how to do it, go two genes up, two genes down, enter those coordinates in the genome browser. And then also download the sequence for that, because we're going to use it in the next assignment. See you there.
