Hi everyone, as part of our comparative genomics series, we're going to start with some of the basic steps that you need to do when you are doing a comparative genomic analysis. One of the first things we teach is how to help you use the global search function to create a genome group. So here in the PATRIC home page, you can see this box here is the global search box. When you're on any page, let's say I go here under this page, the global search box occurs here. So it's on any page that you see in PATRIC. So let's first find some things. I've got an example for you, so a list of genomes that you can use in the global search box. So let's go to workspaces here and click the Down Arrow, and then let's go to public workspaces. I'm logged in right now, as you can see here, and you will need to be logged in to do this exercise. So when I'm logged in it will look different from what you see when you're logged in, because these are all the workspaces that are shared with me. But we all have this in common. Every user of PATRIC has access to the PATRIC workshop folder. So let's click on that and open it up, and let's click on the folder that says Protein Family Sorter. This is all the Protein Family Sorter is an essential tool in the comparative genomics section. So we're going to be showing that in these series of videos. Today, I'd like you to click on 39_Brucella_genomes. And you notice when I click on anything, any row, be it a table or within a folder in PATRIC, this vertical green bar is populated with a number of icons that indicate possible downstream functions. I can edit the type of file this is, which right now here we can see that it's unspecified. I can move it, I can copy it, you cannot rename it because you don't own it. It can be deleted or download, so we want to download this. So let's just click on that. And it looks like it's downloaded. And here's the list of genomes that we're going to use in the global search box. So let's talk a little bit about what these are. These list of numbers are unique identifiers for individual genomes. Now, there are certain things that genomes can be named. For example, mycobacterium tuberculosis, that's a name for a species, and within that species there is a very famous strain called mycobacterium tuberculosis H37RV. Now that name, the name can be broadly shared. In fact, that there are currently 4 genomes in PATRIC that are named mycobacterium tuberculosis H37RV exactly. And there are 14 genomes that have H37RV as part of their name. So across all of those genomes, even though they share the name, this identifier will be unique to them. So that's an important thing to recognize, that this is the closest you can get to any individual genome in PATRIC. So let's copy those numbers, there are 39 Brucella genomes there. And let's go back to the home page, which we can do get to by clicking the PATRIC symbol here, just because I like the real estate that is available on the home page for the global search box. So let's paste those numbers into the box, and we're going to ask PATRIC to find those. Let's click here after all data types. Let's click on the down arrow, and it shows you what you could search for. We want to narrow the search, we don't necessarily want antibiotics or taxa or specialty genes, we want to find these genomes. Let's click on that. And then here, we have another way to narrow the search. Let's click on that and we can look for all terms, any terms, all exact terms. Let's click on any exact terms, because I want to see these numbers exactly. So click on that. Now, we've fine tuned the search and we can click on this magnifying glass here that will launch the search. Very quickly, it gives us the list of genomes. So look, it says there are 39 genomes and these are the numbers. Let me open that again and let's look at, so you can see that these numbers here should match these numbers here. One of the things you can do in PATRIC is any genome, when you're in the table worm here, you can click on any of these column heads and that will re-sort all the data in the table alphabetically or numerically, depending upon that column. So it can do that, and you can see I've these number of Abortus genomes, a Kaneis genome, bunch of Brucella ceti genomes and inopinata melitensis. So these groups bands what we know of as the classical Brucella. So that's the quickest way to use the global search function, and with genome identifiers to get a specific list of genomes that you're interested in. As a practice, what I would like you to do is go back into the public workspace and I have a text document called ancestral Brucella. Why don't you try that and see which genomes you get there, and see if it meets the number that is in the text file. Keep watching my next instructional video where we'll show you how to create a genome group, once you're at this list. Thanks for watching and thanks for using PATRIC. Okay, here's your first assignment. I want you to use global search and make sure that you can find different things. Now, during the course of each of the assignments that follow each of the segments, all of these are sort of interconnected, so go ahead and use the global search. But then don't close the tab, leave it open, go watch the next video, and then the next exercise builds on that, through the whole thing through the Protein Family Sorter. Each of these things is an iterative step in these assignments that builds upon what the previous one does. So using the global search either on the home page or at the top right of any PATRIC Page, I want you to enter the term Unicycler. How many genomes are returned? How many of those genomes are public and how many of those are private? Okay, and then keep that tab open because you're going to need it for the next assignment.
