Okay, so you've done your assembly and you've got a contact file or you've uploaded the contact file. What you really want is an annotated genome, so you can use some of the powerful comparative genomic tools in PATRIC or build a tree, or use it as a reference genome for your variation service job. There are a number of things you can do, but often the most important piece to many of the functions in PATRIC is that annotated genome. So, let's step through submitting a contact file for annotation in PATRIC. Let's go into services, click on that tab and then find the word annotation and click on that. This takes us to the graphical user interface where you can submit your genome annotation job in PATRIC. Notice up here there are information icons that give you information about the service. If you have data in your workspace, you have a contact file in your workspace, click on this folder which will give you access to your home directory, where you can drill down and find the contact file that you want to upload. Or if you know the name of it, you could start typing it and see that. Or if you uploaded a contact file recently, if you click on this blue arrow, it'll show me the ones I uploaded the most recently, contact files back to more in the distant past. I want to annotate this guy, so I'm going to click on that and there he appears. Now, there are just a few steps involved in submitting an annotation job. It's really easy. The first thing you have to do is figure out the domain. Well, I know that this is a bacteria that you can also annotate archaea or bacteriophages, and also viruses, but these are bacteriophage genomes. PATRIC has a really awesome sanitation pipeline for that, but just for bacteriophages, not for viruses. So, let's click on bacteria. Next, we need to assign taxonomic name for it. I'm going to mouse over this question mark. You can annotate a genome and just call it bacteria, and you'll get a fine annotation. But PATRIC provides two different types of protein families. We have global families that cross the genus boundary. So if you annotate something just as bacteria, you'll have global families. But what we also provide for more indepth fine grained analysis are local families, which are the genus and below. So, you really need at least the genus name to get those local families. Let's say you don't know what the genus is, it's something new to you. Later on I'll tell you how you can use PATRIC's taxonomic classification service to give you a hint of what the organism is. But for now, let's assign a taxonomic name. I know who this guy is and I can start typing the name of it. And it's Wigglesworthia glossinidia. And you notice I didn't have to write the whole thing, which is good because I'm a terrible speller. So I could click on it an once I did that, it did the taxonomic ID as well. If I'd known the taxonomic ID, I could put that in and then it would auto fill the name. Now, you notice the output name has the genus and species here. I need to have my identifier on there, so I'm just going to copy and paste that so I know where it came from. And this will allow me to distinguish between what is my private annotation, my private genome in PATRIC, when I compare it to the public data in PATRIC. So we're almost there, we still can't annotate. We just have two more things to do. The genetic code used in the annotation service is an important thing to assign. So, let's click on this down arrow here, and archaea in most bacteria get code 11. Four goes to mycoplasma, spiroplasma, aneury plasma, and then there's 25 for the candidate division SR1and gracilibacteria. Well, Wigglesworthia is under most bacteria, so I'm clicking that. One more thing, well, two more things, we need to assign an output folder. Let's create a new one. If I wanted to create a new one, I could go in here and create a new folder by clicking here and create that. If I have a folder where I want to store it, let's put it in a contig folder, and then I click OK. And there's the folder here, so I'm just going to put it in there. And now, last, we have to determine the annotation recipe. So click on this down arrow, we can choose default or phage for bacteriophage. This is a bacterium, so I'm going to choose default. Now the annotate button is blue, we can click on it and submit our job. And that is the easiest way to submit a job in PATRIC. And the annotation job is submitted and it's off. And you can monitor the progress down here on the jobs monitor. So mousing over that shows me that the sanitation job and another one I have is in process. And that is the dead easy way to submit an annotation job in PATRIC. And in the next video we'll show you how to monitor the job and look at the results. Okay, you have the data, you have the facts, now you need your assignment. So, this assignment is actually a little bit complicated. The first thing I want you to do is submit an annotation job using that MOOC-Test contigs file. There's going to be one part of it, the genus, go ahead and put Brucella in there. This is from a PacBio read, an assembly of that, and it's a nice little assembly. Secondly, if you took all the assembly tutorials, what I want you to do is submit the context from each of the completed jobs. This is going to be part of a larger exercise that we do over the course of this course, that shows you how you can judge the quality of particular assembly, a particular genome, an what role assembly plays in genome quality. So, like with the last one, this one you don't know the genus. I'll just give you a hint, you can put in Escherichia as the genus, and remember to provide the jobs with unique names so that you can identify them later. This is the table I filled out from the assembly, so I'm using the contig files that came from each of these and we're going to do later comparisons of them. So it will be good for you guys to do this. And when I named them uniquely, well, the genus name is filled in, but it identifies what the reads were identified as, and the assembler, so that we'll be able to tell them apart. Good luck. This is going to take you a little bit of time to do, but I know you're up to it.
