So you've run, either your reads, or your context through the comprehensive genome analysis service and Patrick. Now, after you got that, your genome is part of the Patrick System, it's only available for you to view, but you can compare it to any of the public genomes and Patrick, or any of the private genomes that you have. So how do you find that genome? So with that, we can show you what it looks like. Well, you could go down here and click on your jobs monitor. You could search for it in the global search, or you could go up into workspaces, or you can click on my genomes, or my jobs. I annotate a lot of genomes and I can't often remember exactly what they're called, because I use SRR numbers. I can't remember all of that, so I often like to go through my jobs. But if you gave it a distinctive name, might find it more easily that way. So when I want to view something, you highlight the row, and this populates the vertical green bar with possible downstream functions. So I want to view this job. So I click on view, this takes me to the job landing page, which I've discussed many times, another videos, and you're probably bored to hear about it. One thing I never discussed was this interesting little blue eyeball up here in the upper right corner, staring at you, that I haven't clicked on yet, so this will give me direct access to my genome page, and so, let's click on that view, annotated genome. It's going to overwrite this page, and show you all the information associated with your particular genome in Patrick. Let me point out that there is a lot of stuff that comes with the genome annotation and Patrick. We can't fit it all on one page, so we have a number of tasks here, so that you can see all of those different things. Another thing that I should note, is that here, you can share the genome with your working with a group, you want to share this genome with other people. You could click here on the share icon, and you could start adding lab members, or whoever you want to share the data with. You just know their last name. You can put in name in. Yeah, this is a guy I want, and I can give him you, or edit privileges, depending upon, if you're teaching a class, he might just want it to be you. If it's a collaborator, you might want it to be edit, so you can say add user and save that. And then, in awhile, you'll be able to CRC, and it shows who has the privileges to view this genome. So let's talk a little bit about this page with any annotation, and Patrick, it comes, here's the name. It tells you where your genome is within the great tree of bacterial life. The taxonomy up here in the breadcrumb, there's information about the genome itself, it's quality, how many context it has, when it was inserted into the system. There is also details about the genomic features, the number of genes called, repeat regions here in an RNA, notice that there's Patrick annotation, but no RefSeq annotation, because this is a private genome. Protein features, getting into the specifics on that. How many hypothetical proteins, proteins with functional assignments? All the information here, and these are all hyperlinks, so you could go directly to that information. And then, specialty genes, image genome annotated, and Patrick is blasted, or blatted against specific databases for variance factors, antimicrobial resistance, genes, drug targets, transporters or human homologue. So we have that kind of information for you that you can drill down into. You'll also notice that we have a number of tabs here that show different things about the genomes, including if there are antimicrobial resistance phenotypes. The phylogeny, your organism won't be included in it, but it shows you an overall phylogeny of either the genus or the order. There's a genome browser, a circular view. Sequences, or the context themselves, and it tells you how big they are, and how many genes are called on them. Features are a list of all the jeans, the specialty genes. If we were to click on that. Just because this is kind of interesting for people, it. Tells you whether they were a blast search or Kamer Search, which we do for some of the antimicrobial resistance. So I could click here to zero in on that and filters and if I wanted to see everything, you can see that there the blast ones which show you the e value and the identity. And also links to publications that describe this gene as in this case a transporter which I can see from this top row here or as in this case, this one is a variance factor. And I could get to the direct publication here. And look, you can see here there's some information about this that appears when you select one, it's time that tells you the information about those things in that lower, yet better in that selected gene. So this is a valuable thing, but if you wanted to see everything that was identified by Kamer search compared to that, you could click here and that would show you what the Kamer search were and what they were hitting within this particular genome? Protein families, we have special tabs for that. For pathways and subsystems. Now subsystems are a special annotation project of grouping jeans together that function together. Like maybe their pathways. Maybe their part of the transporter system? We have the curation team that big into these kind of things, so this might be something that you want to explore as well. Transcriptomics, we won't have any your private she knows, but for some of our more that we have a lot of data for, like my so bacterium tuberculosis, you could see gene expression data from some of the public experiments and interactions. So this is what your genome looks like in Patric. And once it's here and you have all these information at your fingertips, you can do a lot of things with this. You can build trees, including your genome. You can compare the protein families. You can use it as a reference genome and compared snips using reads from, if you're doing an experiment with it. But the first step is you have to get it to this point and have to get it inserted into the Patric System. If you have any questions you need to let us know, but we hope the user service inside us and have fun exploring your genome in the Patric tools. Thank you. Okay guys, we have another assignment. This one I'm going to ask you to do something I haven't shown you before but don't worry, I'll step you through this. The aim of all of this is to get you comfortable with going to the genome landing page and Patric for your privately annotated genome. Clicking on some of the tabs and being able to start manipulating the data that are in those tabs. We're going to start with panel to step through the canoe assembly strategy that had four raccoon iterations an no pylon iterations. So we're going to take some of the specialty chains from that job and create a feature group for it. You're also on your own, going to do that for the Unicycler that was listening with four Recon iterations and 0 Pylon. And then both Canu and Unicycler that had four raccoon iterations an four high line iterations. It's not that there's anything really magical or amazing that you're going to see from these things, but it'll just get you comfortable with doing it. I'm going to step you through it and I want to go to my jobs and so what did I say? Canu_4_0, all right? So I'm going to go to that job page and then you can see up there. I have the view icon, I could get here from other ways to going through the workspace and everything else. But for me this is generally the quickest. So I'm going to click on that. Let the page load and then remember, we talked about all the different tabs. Let's go to the specialty genes tabs. Any genome that's annotated and Patric is blasted against several different databases. So let's click here on the filters. And rather than doing all of it, because 322 genes that you can see here. That's a lot. I'm going to click on some pretty well known databases just to see that card. Card is the comprehensive. Antibiotic resistance database. It's one of the gold standard ones by MacArthur up in Canada. So let's click on that. BFBB, that is the variance factor database. Another gold standard database. And then drug bank. This is just for fun. We blast against that so you can see if anybody is using a particular gene in your genome. For if it has similarity to anything but people are trying to develop drugs against. So let's click on that and you notice that after I click on each of these, we went down from 300 to 307 to 116. So this check box up here at the top. We're going to click on that in a second. Note that the vertical green bar is empty. I click on the upper checkbox and suddenly. I have the possibilities of what I can do with this data appear. I can go to the features page, I can see the genomes. I can get the fast a data, I can build a multiple sequence alignment. I can look at different identifiers. I can see if any of them are involved in pathways or I can create a group. So let's click on that. So I click on that and it says. You want it added to an existing group or click here and click on new group because this is a new group. And I'm going to call it canoe 4 zero special gene, just so I can say that. And they will be saved in my workspace under that, and we're going to come back to it later. So go ahead and click that. And then it gives you a little message you if you created a group you created a group. That's one down. Now you guys, go through and do the next one. I know you can, have faith in yourself. Good luck.
