SnapGene feature highlights: October 1, 2024
Transcript
Good afternoon, and thank you for joining us today for SnapGen's webinar with Dr. Evan Starr. My name is Axinia Radeva, Manager of Research Computing Services at CUIT, and our team supports researchers by providing advanced computing solutions.
We work to ensure that you have the right tools from high-performance systems to optimized workflows to drive your projects forward and achieve groundbreaking results. The RCS team offers a diverse portfolio of services to support your research, and we'll put our URL in the chat. If you're interested, you can visit our website.
User training can support our key components of facilitating effective use of our resources and services, and today's session is designed to address that need by offering valuable insights from experts in the field. Feel free to ask questions, share your experiences, and make the most of the expert advice available today. I would like to quickly recognize Jessica Eaton, who is a research analyst on the RCS team and the organizer of today's workshop, and I'll pass the floor to Jessica, who will make a few announcements and introduce our speaker.
Jessica, the floor is yours.
All right, thanks, Axinia. Yeah, just a few housekeeping things, folks.
So you may recognize my name from the purchase and license distribution for Snapgene, but if you're not aware, one of our services is gathering everybody who uses Snapgene at Columbia together to get a bulk discount on the software. Normally, the licenses are like $295 a year, but if you work through us at CUIT, you can get it for about $135 a year, and we renegotiate that price each year. We also do a similar program for GraphPad Prism, if that's something that you're interested in.
One thing that is new this year is we have finally put all this information about discounted software together on a single page and how to buy it, and so I'll drop that web page in the chat, too, just so you can know the fastest way to getting your discounted license rather than just emailing me. All right. Also, as we mentioned, this session is being recorded.
It will be posted to our training page, and this is our planned agenda today. Just to check, is anyone here just getting started with Snapgene or doesn't even have Snapgene and is, like, considering it? Feel free to, like, raise your hand virtually or comment in the chat. If you can just do that to let Evan know if, like, a general very intro to the tool is needed, that would be good.
Looks like maybe everybody has some awareness. Also, I'll note that I did pull the topics that a few folks submitted with registration and put them at the bottom, so we're sure to get to them, but it's likely Evan will integrate these more organically earlier in the presentation, but those were some things that people had specifically asked for. And without further ado, I'll introduce our guest speaker, Dr. Evan Starr.
Evan has a Ph.D. from UC Berkeley in rhizosphere ecology, and he's worked as a soil carbon scientist and microbial ecologist. He currently works at Dotmatics, which is Snapgene's parent company, as a field scientist, and he's both a subject matter expert on Snapgene as well as a seasoned researcher. So if you have any presentations throughout the session, feel free to unmute yourself and ask, or you can put them in the chat, and then we'll bring them up.
Okay? And, Evan, it is yours. I will stop my share. Perfect.
Thank you, Jessica and Xenia. Thanks so much for inviting me. Really happy to talk to everyone.
We're going to go through Snapgene today, but as Jessica said, just unmute yourself, interrupt me with any questions. I try and keep these sessions as informal as possible and want to make sure you all get the most use out of it. If you don't want to unmute yourself or interrupt or anything like that, use the chat, and I'll try and keep an eye on that.
And if I don't see anything, folks are welcome to shout out and let me know if they do see anything there. So thanks for having me. Evan Starr, happy to talk about Snapgene today.
So Snapgene, as you all know, our molecular biology, cloning, general molecular biology toolbox. And so we're going to go through some of that, and I'm really happy to answer any questions, because it sounds like a lot of folks are very familiar with Snapgene. If anyone is not super familiar and is just getting started with Snapgene, or if you've got colleagues that are just getting started, we actually have a thing called the Snapgene Academy, and this is a great resource on our website for getting started.
And it's got videos. It's got written guides for all of the different common use cases within Snapgene. And it even has some, like, if you're ever teaching someone, it actually has, like, the science behind all of these different cloning tools and common molecular biology tools.
So Snapgene Academy is a great place to start to really get to learn how to use the program. What we currently have is Snapgene 7.2, and I'll introduce you to some features that have come out recently. We've got some new features that have come out, and what we also have coming out is in the near future.
We've got Snapgene 8.0, so a new version. We come out with new versions every year with some cool new features and introductions. So you're not obligated to update, but it is, like, safer and has all the fun new cool tools in it.
So Snapgene 8.0 is going to have a little bit of a UI redesign or a user interface redesign just to make it even easier to use. Some things are getting moved around, but we will show you where all of these things are getting moved around, and we'll try and make it as easy as possible to transition to this new user interface. There are going to be some new features included, like some of our homology annotations, and then one thing that is actually pretty exciting is that if people are familiar, we used to release a separate software called Snapgene Viewer.
That was basically the unlicensed, unpaid version of Snapgene that you could download, and you could basically open up files and view them, you know, like, do all of the kind of, like, viewing, but none of the editing with Snapgene files. So that's great if you've got a colleague who just wants to be able to view, say, a GenBank file, but doesn't want to go through any processes to get the full version of Snapgene. And so now that's all going to be bundled in one program.
So basically you can run Snapgene, the full program, without having a license, and you can still view everything, you just won't be able to necessarily do any of the operations that we're going to be talking about today. So that's some of the new stuff coming out in Snapgene 8.0. If you are interested in becoming a beta user or anything like that, you're always welcome to reach out to us. I was interested to hear people's thoughts and opinions about these types of redesigns especially.
Perfect. Just shout out again if anybody has any questions, but those are some of the new capabilities that we're releasing. I wanted to do a little bit of conversation about annotations, because that's really important, and there was also a question that came out with annotations.
And so what happens with Snapgene is we can, of course, open up our little folder here. And so this actually points to a folder on my computer. I'm using a Mac, so it's going to pop up right there.
And we've got that folder with all of these individual files in it. Sometimes you will get sent, for instance, like a sequence that's just a raw sequence of nucleotides, or you'll do some sequencing, anything like that, that you might want to get some annotations on. And so if we've ever got a new sequence, we can go ahead and annotate that directly.
So all we need to do is up here at the top is click our little New Sequence icon, or we can go through the File menu. In this case, it's going to be a DNA file. And so I'm just going to create a new DNA file.
And it's really easy to copy and paste that sequence in there. So what this is doing is it's copying and pasting my sequence in there. It's automatically creating a circular file and detecting some of my common features.
But if you've got a different topology, we can always change this around if you want. And then we'll give it a new little name, so New Plasmid there. And we can go through all of the techniques for adding in these new annotations.
So what you'll see is a bunch of annotations have popped up on this sequence automatically. Really common are plasmid types of features, right? Our restriction enzymes and our antibiotic resistance and our origin, all of that will appear. What we've got is a nice handy little drop-down menu where we can set our percent match.
So 96 is kind of what Snapgene thinks of as the standard. But we can always change this if you want to be either more strict or less strict with your annotations. And so if we come up to 100%, I think just about everything is going to be matching very closely.
But we can annotate all of those features on there. And if you didn't want to annotate any of them, we can uncheck them. And I'm just on my laptop screen, so you'll see that this stuff is kind of cramped.
If you're on a larger screen, it'll be a little bit easier to see. Or we can come into this more detailed view and see all of that metadata and the translation information that's coming along with that sequence. So really easy to just go ahead and annotate brand new sequences that we get brought in.
And then I'll talk briefly about adding in new custom features to annotate to and how to share those with colleagues. But does anybody have any questions about just that very basic, just annotating using those standard features? No? Perfect. So the other couple of options for annotations that we get are, if you ever wanted to, we can always select a region of DNA or RNA or protein.
Or we might have either one section or a couple of different sections. And all we need to do is go into Features and Add Feature. And so basically, all of the annotations in Snapseed are features.
And there are a lot of different ways of modifying, adding, removing all of these different features. So we can come up here into Add Feature. And we'll give it a name.
And I'm always really bad at naming things. I'm sorry, everybody. So we're going to call this a cool domain.
Great. So that's going to be the name of this feature. And then we can give it a type.
So there are a bunch of built-in common feature types, right? So common chunks of DNA or RNA or protein that we might see. But you can see that I've also added in some custom ones. For instance, like if I'm doing some antibody work, I might have my framework region or something like that.
And some of these are treated a little bit special. For instance, if you've got a CDS domain, that will be automatically translated in your annotation. But I'm just going to call this a miscellaneous feature because I don't want to get too complex.
If we wanted to, we can always split this feature or change the directionality of this or do any complex things with how we're adding this new feature. And we can add any metadata that we might want to add there as well. And again, this will all be carried on over to any new features that we annotate using this.
So easy to annotate a new feature like that. And as long as I save it, we will have this saved in there as our new domain. But the important thing is to be able to then re-find this in other sequences, right? So you'll probably have other sequences that you're working with and you want to find this on those.
So instead of manually going through this whole process, we can instead add this to our common features. So basically, we will have a whole database of these common features, and we can start to add in new sequences to our custom features. So now if I add this, then every time I run that previous detect those common features, this new domain will appear.
And I see that someone is off. Do you have a question? Can I have a question? Yeah, perfect. So there are some cases that I want to leave new feature nameless, but I think it's not possible in Snapchat or is it possible? Nameless? That's a good question.
I don't think we can keep this without a name. I mean, I tried. I couldn't manage to do it, but you have to enter something.
Right. You do. Okay.
But you would prefer to not have anything in there. Yeah, sometimes. Because sometimes I just highlight those different regions with the same color, with the same name.
There is no point giving a name, but it forces me to give a name all the time. Right, right, right. Yeah, that's a good, that's an interesting use case.
So part of my job is obviously to come out and teach you all, but also to collect information from the field about what would improve that. So that's a good idea is to be able to make features basically without names. So part of this is to teach you all, answer any questions.
If you do have any suggestions or anything like that, you guys are always welcome to reach out. One thing that you could do is instead of making, you said you've got multiple different sections all with that little chunk, you could highlight the whole thing basically, and then split it up into multiple different kind of sub-annotations. But I think even then, they'll probably have to have names with how we currently work this.
So we would have this be a large chunk of DNA, right? And then we can actually start to split this feature into whatever segments you want, and have this be basically whatever four or multiple different sections. And we can start to recolor some of these chunks here. This is a little bit more manual where you got to like move the numbers around, but that could be a good way to start to kind of highlight some of these chunks of DNA.
Thanks for the question. Perfect. So with those features, we talked about going into features and detecting those common features.
We can also add those common features. And then really important part of this is when we come into Browse Common Features, we can always import and export our standard features or those custom features. So you can see I'm very bad at naming these things, but we could always export all of our features.
And when we send this to a new colleague, they can import them, and then they will be annotating all of those features that you are working with as well. So that's one way to just kind of start to share annotations. It'll share all of that metadata, all of those annotation types, all of that kind of thing.
Perfect. Any questions about other questions about annotation of sequences? No. Great.
So, and I think that that addressed one of our questions, unless anybody doesn't have—unless someone has a follow-up. Setting parameters for identifying common features is basically being able to use that Detect Common Features tool and setting a different threshold match for these different features. So you can use that, and we can always set this to default.
And if you don't like any of these, we can always turn them off. And actually, here we can see we found a couple new features on this chunk there. Perfect.
So I was going to move into some cloning operations, if that works for everybody, unless anybody has any questions about annotations. Great. Along with the Snapgene Academy, we've got articles and videos for every different possible type of cloning operation, but they're all going to work pretty similarly.
So if you ever wanted to know more about any of those operations, it's all going to be under Actions. And if we come down to any different technique, you'll see a little link out to any of those videos. And so that's a great way to kind of learn about any of these different cloning operations.
So here's a very generic example of doing some Gibson Homology cloning. So all we need to do is open up our Backbone and come into Gibson Homology. In this case, we're just inserting one fragment, but if we wanted to, we could insert multiple fragments next to each other.
So I've got my Vector open, and I'm going to click Insert Fragment. And so this has been selected as my Vector. If I had clicked on the wrong thing, we can always choose a different Backbone or Vector from down here.
And then we're going to, just like in the lab, we're going to linearize this sequence however we want. We can either use restriction enzymes or outward-facing PCR primers. So whichever works for you.
In this case, if we wanted to graft this onto our GFP, there's a nice NCL1 site right here that we can work with. If you wanted to get deeper into the sequence view, we've also got all of those same options as when we're looking at that viewer, again, down in the little cloning operation. So that can get you really precise into where you might want to clone something.
So I've clicked my NCL1 site, and now we'll go into our Fragment tab. And so that's whatever we want to insert into here. And we can choose from either any open documents or anything within basically our computer, anything that you can have access to.
And so here we can come to this map view. If I just wanted to insert this gene and not the upstream and downstream stuff, I can just click on that gene so that it's highlighted, and now that will be basically what we'll use as our template for generating our PCR primers. All we need to do then is go into Product.
So we've got our Vector and our Fragment, and we choose Overlapping PCR Primers. We can, of course, set all of the different temperatures, the amount of overlap that we want. We can even regenerate upstream and downstream restriction enzyme sites if we wanted to.
So if we go ahead and run this, we can choose our primers there, and it will automatically generate them. If you ever wanted to, we can go back and forth between all this. So if you didn't like this end product or if you wanted to rename any of your primers, you can always do that as well.
So now all you need to do is save it. And so good naming conventions, always important. So name this something that will make sense for you.
But this will create a new file that's got that end product that we've now cloned this gene into. So go ahead and click Assemble, and now we've got this assembled.dna. Perfect. So some fun things here.
We can turn on coloring, so that will color something if it's been newly added into this vector. We can come down into our sequence view and get a little closer look at our sequence and see if we like where it's being cloned into and what is happening. You'll probably notice that I forgot to remove a stop codon, so you probably want to change that in here as well.
If we wanted to come down into primers as well, there's a different tab here for primers. And what this will show you is basically, in our case, our two different primers, where they're binding on our sequence and the melting temperature. And you'll see that this one actually has an off-target hit at a pretty high temperature.
So maybe we don't really need to worry about that, but that will call that out for you just in case. One of the newer features of SnapGene is we're actually being able to show the structure. So structures of small chunks of DNA or RNA.
So depending on if you want to work with CRISPR guide RNAs or tRNAs or primers, we can always click Show Structure and see a nice little structure of that sequence. We do a couple of different calculations of the structure, and we'll give you a bunch of stats down here. This is just for the monomer, so we can look for any hairpins.
But we can also look for homodimers within our sequences as well. So some fun, fun features that we've got now with SnapGene. We can click on this guy too and do the same thing and see if we've got any hairpins or anything like that.
And all of this can be exported as an image or a dot bracket or however you might want to export this. And we can always change any of the parameters down here. For instance, change our temperature.
And you'll see the temperature is listed up there at the top. So fun new feature. If you have any thoughts about new ways you want to see structures or different kinds of structural stuff, let us know.
That's now a capability that's built into SnapGene and something we can continue to expand on. One of my favorite parts, and people who use SnapGene will probably know about this, is the history view. So basically, when we do any cloning operation, all of the history of that cloning operation will be saved in this final file.
And so what this means is that we can either resurrect any original documents, or if you send this to someone else, they can open it and they will see basically all of the operations that have been done. And this can be exported as an image or as a text. And what I really like is if you're going to have something maybe synthesized, and so you don't want to actually do this PCR or something like that, we can just double-click on any mid-step and generate that file.
And you can see now it's already got those overlaps on there for us. This actually brings up an important point of documenting all of your different cloning operations or any of your different work that you're doing. So one thing that SnapGene actually has is an integration with LabArchives.
So SnapGene and LabArchives are both owned by Dotmatics, our parent company. So this is a really easy-to-use, really customizable ELN that lets you basically drag and drop documents into it. You can import all sorts of fun, cool widgets or anything like that to do all of your work within LabArchives.
And once you get it set up, it's also easy to basically work with SnapGene and LabArchives at the same time. So we can either open up files directly from our lab notebook, and so that's a great way to basically use your lab notebook as a repository for a bunch of different documents. And then it's important to know that when you do, for instance, a cloning operation or make any edits and you save that same document that you downloaded from LabArchives, it will then save that back up to LabArchives.
So that can be a really handy resource for documenting what you're doing or attempting to do. If anybody has any questions about that, reach out to us or the LabArchives team. We have resources for that.
If you ever need to contact the SnapGene team, you can always click Help and ask a question, report a bug, make a suggestion. So we're always happy to hear from everybody. I'm just going to butt in real quick and just let folks know.
I'll put this link in our recap email, but LabArchives is doing a webinar specifically on workflows for LabArchives and SnapGene on October 16th. So I'll send you the registration link. That's that bootcamp thing.
So yes, exactly. Yeah. Perfect.
Thanks, Jessica. And I think they're also doing some stuff with GraphPad Prism too. So GraphPad Prism and LabArchives work together as well.
Yeah. Great. Yeah.
So I, you know, lab notebooks are really important and everyone's going electronic. So yeah. Let us know how you like these integrations and if there's anything else you'd like to see too.
Yes. We can contact support. Are there any questions about cloning operations or anything that we've covered so far? Or the integration with LabArchives, if anybody wants to see that a little bit more.
I would like to see that a little bit more. Perfect. Perfect.
That sounds great. So basically what we can do is within SnapGene, all we need to do is go into preferences and we can set up our connection with LabArchives. And we'll send out, I can send Jessica an email that's got a bunch of different links to this that can be sent out to all of you guys.
So basically we can connect LabArchives with basically using your email address between SnapGene and LabArchives. And so that enables this exchange of files. And so now, for instance, I made that final product wherever that went.
I don't think I saved it. But if I wanted to save, for instance, this file back up, I did some operations that have been done, and I can either go into Snapgene and save to lab archives, and that will automatically pop that file back into lab archives, and that will go to whichever one of your lab notebooks that you're using. So you'll see here I'm saving to one of my lab notebooks and a specific page, and you can see those recreated right there. And so now if I save this back to that document, it will, oh I think I'm signed in as a different user, sorry about that, it will then be able to save that document back up there.
And the same thing is if we go into Snapgene, and instead of save, if we go into, um, if we go into open from lab archives, let's see if this works, I've got so many different accounts for all these things, and we can go into open. So what that will do is it will allow me to open up this file, so I've basically pulled something from my lab notebook, and this could be just a repository of a bunch of plasmids. Now if I made some kind of, you know, chain, I went in and just deleted a big chunk of DNA or something like that, and if I clicked and saved that, it would save back to lab archives.
And I think I've modified my permissions, so it's not letting me do that, but that's basically a way that you can start to work with these files back and forth with Snapgene and lab archives. And I'll send out an article on how to use those two together. Does that answer a little bit of your question? Maybe.
Okay. Oh, perfect. Perfect.
Yeah. And then within lab archives, it's basically like a really easy and customizable way to do a bunch of different, you know, all of your different ELN types of techniques. And then once we've got those files actually saved into our lab archives notebook, you'll see that it is a little document here, and if I click that, it will either download it, or if we come to a different one, we can actually view these within the lab archives notebook itself and actually see the, you know, all the different annotations and get a nice little view of those different documents.
Ah, there's that little eyeball viewer there. It was just cut off on my screen, but basically lab archives has basically that free viewer of Snapgene built directly into it. So if you import any GenBank files with annotations or Snapgene files, they will all bring along all of those annotations.
And so you can view those directly within your lab notebook. All right, perfect. Any other questions about cloning or anything like that before we move on? Yes, I have a question.
Because of my lower outdated version or not, so the cloning, my understanding in which I tried, if you have two restriction enzymes, you type in and you can automatically generate a final construct, right? So the question I have regarding the gene targeting CRE lockspeed technology we often use. So you have a two lockspeed site. Once you add the CRE, when you pop out the two lockspeed can add the gene automatically generate the final construct? That's not specific cloning, but it's a way how you actually manage the sequence from editing, right? Exactly.
Yeah, yeah. Snapgene. And so would you like, you would obviously like to be able to do that within Snapgene, basically replace those chunks within Snapgene, is that right? Exactly.
So what I did is I have to manually find out the way lockspeed are then take out and stick them together. But I hope that Snapgene has a place we can choose. This is a CRE.
And there's a Snapgene, we are automatically looking for where lockspeeds are. Then once you click on it, it automatically generate the excised allele. That is a great idea.
Yeah, that would be a good idea. I don't think we've got a built in, I think right now it would be a manual system, but that is something that would be a handy tool, especially more and more these days to add in. So I'll bring that to our developers.
I can never make any promises about what will be included in future versions, but I think that is a good idea. And so, yeah, yeah, yeah. Yeah, of course.
Thank you. And yeah, we'll, yes, I think that's a good idea. And I think I, yeah, I know what you're saying.
If you do have any other thoughts or if you want to add more details, you're always welcome to make a suggestion as well. And that's always for everybody really valued by our developers. Right.
Yeah. I mean, that's a good thought. Lockspeed, they are flipper like all other like genetic engineering, because people always using Snapgene to manage their pocket alleles.
So when we have flux allele, white type allele, we want to generate a knockout allele automatically rather than going to a nucleotide by nucleotide taking out. Right. So, so you Snapgene is a fantastic tool to do this if it's doable.
Yeah. Yeah, it is. Yeah.
Let me, let me also take a look and make sure we don't have some secret little way, secret little handy trick to do that too. So I will. Yeah.
Oh, sorry. One second. Thank you for all the comments.
Everybody really appreciate it. Perfect. Anything else, any other questions about cloning or different synthetic biology kinds of things that we want to talk about before we move into maybe some primers and some agarose gel kind of stuff as well? No.
Okay. Perfect. So primers, I think I've discussed this with folks as well, basically within Snapgene, just like with making our features, we can select a region and manually generate primers within our sequence.
You'll see that we've got that length and the melting temperature. And all we need to do is select that region and come into primers and add primer. So easy to add top or bottom strand, rename that primer with whatever we want.
Always good to add in a description. And then if we want to modify this, so if we want to make a mutagenic primer or add in any enzyme sites or different little tags or anything like that, we have those automatically in here for you. So we'll have the five prime end and the three prime end marked for you.
And you can always either type directly in here or you can use any of these insert kinds of things here as well. The same thing goes for doing stuff directly within. So if you wanted to either delete, you'll see that we've got this little icon there where we're deleting some nucleotides or we can add in more as well.
And so we can start to generate these primers and you'll see that all of our percent GC and our melting temperature and stuff will all be recalculated. So easy to add primers to our template DNA. Again, it will all have that metadata that's associated with it.
But a lot of times folks are storing their primers basically in Excel is what everybody that I talk to uses. We're eventually going to try and build up a database for primer design and primer storage to be able to like kind of centralize all of that information. But right now we're just relying on Excel like everybody else.
So basically if you've got a database of primers and you want to see if any of them match to your sequence, all we do is go into primers and import primers. And this can either be from a different snap gene file. So if we've got two different snap gene files, we can see if any of those primers on that snap gene file match to our new file or we can import these primers from a list.
And so there are a lot of different ways to denote this format. It can be in a CSV or a fast file, anything that you might want, even from a clipboard. And then we do have these little options.
So if you're like, hey, I've got a giant list of primers, but I only want to find unique binders, we can click that on. Or if we want to add a little bit of wiggle room, we can look for maybe not a perfect match for the whole primer, but add in maybe a little bit of mismatches there as well. So a number of different ways to match all of your primers, and we can add them all to our sequence.
Once we've got them all added, of course, we can always export our primers. So go into our little primers tab, and we can select all of them and come into primers and export selected primers. So if you wanted to export those to then go purchase them or anything, you can do that as well.
And we can choose which metadata we're going to include along with that. Perfect. So it's a little bit of the primer work.
You can see if we've got any mismatches or weird binding sites, you'll see that. And again, we can always double click and modify, rename, whatever we might want to do with those primers. With primer work and with restriction enzyme kind of stuff, we start to get into our agarose gel kind of work.
And so we can start to talk about that. So if we go into tools, we can go into simulate agarose gel, and that will bring up this new little tool. And so we can choose a variety of different files that we want to bring in.
We can bring in those ones. We can bring in all of these. We can bring in a bunch of different files, and we will generate a new gel file.
And from this gel file, we can select each of our different wells and choose which primers we want to use within this sequence to amplify that or which. So here we're amplifying with PCR, or we can cut with different restriction enzymes. So you can either find those or use these little buttons to annotate some different restriction enzymes.
So a number of different ways that we can start to simulate these agarose gels. And then really handy too is we can always duplicate wells. And so those will duplicate with those same settings.
So if you needed to change something, you can always do that there as well. Once I save this, we'll save it as basically a gel file for Snapgene that Snapgene can then open. But we can always export this as a gel image, export a fragment list, export the DNA, whatever we might want to do from that agarose gel.
And this is handy to save back to maybe your lab notebook. So yeah, lots of features for agarose gels. And then we do a lot of science behind actually working out the correct agarose percentage and adding in different ladders that you might want to use.
So we can choose a variety of different ladders from common distributors there as well. So some handy ways to start to verify your data. One question that did come in was also talking about multiple sequence alignments for primer design.
So so far we've just been doing single sequences for doing primer design and all of our work. But Snapgene does have tools for aligning sequences as well. So that's both taking our reference sequence and aligning a Sanger sequence to it or doing a multi-sequence homologous alignment.
And so we'll talk about that real briefly and then we'll open it up to some questions. Basically what we can do is we can select a variety of different, in this case these are DNA, but they could be RNA or protein sequences. And I've selected all of them and we can align these sequences.
And so one of these new features has come out where we can just automatically align all of these sequences. So that will pop through and we can view that alignment. We can modify this in whatever way.
Say if we want to compare everything to one sequence or compare it to a consensus sequence, change the coloring or view any of our annotations, we can do all of that. One thing that we can't do is generate primers directly on these alignments. And so that was a really good question because I think that would be a helpful thing.
But what we can do is once we've made an alignment, we can always export this consensus sequence. And so that's a great way to actually generate our consensus sequence. And we can open up this side panel and choose how we're generating this consensus sequence.
So if we want it to be more strict or less strict, we can change that percentage of the threshold of what we're calling a nucleotide. And then we can right-click and export our consensus sequence into a new document. And that would be a handy way to then generate, basically, design primers based on that consensus sequence because then we would know if we've got dashes or if we've got non-homologous sorts of regions within there.
So that was a very quick little tidbit on making consensus sequences from multi-sequence homologous alignments. But then you could, of course, use that consensus sequence to then design your primers. All right.
I've been talking for quite a long time, so I want to leave room for any questions that people have. So does anybody have any things that they want to cover, comments, anything like that? You're welcome to unmute yourself or type directly in the chat. And I'm sure whatever questions you all have would be really valuable for everyone else as well.
Well, as people think about their questions, there are a variety of different tools that we weren't able to talk about. And a lot of those are going to be on those websites. And we can look through these.
There are some articles that I can send out, too, for using some other common tools that people might want to use, like choosing alternative codons or maybe using BLAST from within Snapgene as well. Did someone unmute themselves? Is there a question there? I think it's just me. Or is that Jessica? Perfect.
Perfect. Well, I went real quick there at the end to leave room for questions. So if anybody does have anything that I have already covered and wants to know more about, you're welcome to shout that out as well.
Yeah, we'll hang around here if anybody wants to chat. And then just look for the follow-up email from Research Computing Services with the links that Evan and I have both been mentioning. But yes, thanks, everybody, for coming.
And thanks again to Dr. Starr for the overview. It's been helpful. Yeah, thanks for inviting me, of course.
I'll stick around for the last 10 minutes and answer any last-minute questions. And then if anybody does want to find, I've been mentioning a lot of tools and going pretty quick. And so one really handy technique for finding some of these tools within Snapgene is just doing directly within this search.
So if you're like, OK, I know I want to find non-cutters, but Evan didn't mention non-cutting enzymes. If you just search within here, it will tell you all of the different ways, like places that that comes up. And so for instance there, we've got that nice, funny little floating guy.
And we will see our non-cutters. Oh, great, we've got a question. Can you show us how to align DNA to a chromosome? Yeah, of course.
Would that be like a small chunk of DNA or a Sanger sequence or a NBLAST? Perfect. Oh, we've got so many questions. Awesome.
Yeah, so if we've got a chromosome, in this case, this is just a plasmid, but this will work exactly the same. So if we've got a plasmid and we want to align a Sanger sequence to it, all we need to do is go into actions. And here, or no, sorry, we will go into tools.
And we will align to reference DNA sequence. And so this is one of the ways that we can align multiple sequences where they're entirely homologous across the entire end. Or this align to reference sequence is where it will determine where one or more Sanger sequences match to our sequence.
And so all you need to do is import your full chromosome. And then we will come down here and choose any of our AB1 files to map to. And that will automatically determine the correct directionality and where it matches along that whole sequence.
So you'll see this view here that kind of gives you a global overview of where that sample is, sequence is. Or we can click this sequence view, and that's kind of the best part where we can then actually see these traces and where they match on our sequence. And so if we scroll along here, you will be able to see if there are any mismatches that appear.
And we can even use these little arrows to hop to any of those next mismatches that might have occurred. Once you've got that, there are a variety of different things that we can do, like replace any of those nucleotides. If you wanted to basically make a new document using what you have made your source of truth, we can do that.
We can add in more, you know, Sanger sequences. This is just one, but we can do multiple all at once. You just select them in that little tool.
Yeah, perfect. And I'll send a follow-up with that. That will also be saved in this little tab.
Can I ask another question? Yeah, yeah. It's more of a suggestion, probably. So I wonder if a SNAP gene could integrate with Ensembl for certain gene structure.
For example, if you want to import one of the gene genomic sequences with exons and introns, can SNAP gene automatically annotate the introns exons for us? That would be really cool with Ensembl. Yes, SNAP gene does not have kind of that capability in terms of integrating or like annotating. It'll annotate like those subdomains.
So if you download a gene that has intron exon kinds of domains within it, within that one feature or multiple features, it will then annotate them as they get brought along, but it won't necessarily be like intron exon aware, you know, where it could be like, oh, it would make sense like homology wise that this would be an intron, but really that would cause a, you know, frameshift mutation. And so it probably that intron is one further or a little bit further or something like that. So it's not going to be maybe amino acid and translation aware, but it can do homology based annotations in that way that we talked about annotate from custom database.
Yeah. I just wondering because most of the gene structure, intron exon sequence already will define the Ensembl. So if SNAP gene can automatically import those information and automatically annotate for the users, that would be really time-saving.
Yeah, that would be time-saving. Perfect. Well, I'll bring that to our product managers.
That's a good idea too. Okay. Awesome.
Thank you. Yeah, of course. Thank you for the questions.
There's another question about BLAST and one about moving. Yes. Perfect.
So for BLAST, what we can do is if we've got any sequence here, all it does is go into tools and this will blast just against NCBI. And so if we've selected a region here, we can blast the nucleotide database, the protein database, translated nucleotide database, or if we select a protein sequence, we can annotate or blast that sequence there as well. So when I click this, what it does is it opens up a nice new little window just directly within BLAST that we can run, and it will have that be named what we had that named originally.
So it's not necessarily running BLAST within SNAP gene. It's just a real handy way of popping that document out into BLAST. And then once we've run that, we can also then, if you export a GenBank file, you can then import that into SNAP gene.
So that was under tools and BLAST. And let's double, let's check if we've got a translated feature. So if we've got a, this is still in the DNA space, can we then, ooh, we can now, even though it's just DNA, genius, or SNAP gene knows that it should be translated.
So we've got our translation there. And so we can either blast the DNA or the amino acid sequences there as well. That's pretty handy.
I never thought about that. Sorry, just an aside. And then there was a previous question about being able to move the DNA, move the DNA along the sequence to change the alignment.
So once we've got our sequences aligned, there are a couple things we can do. If you have basically SNAP gene will automatically trim these sequences. So you'll see I'm able to drag along here and basically expose more.
And so what SNAP gene does is it automatically trims some sequences and that is all by default within this, this little hide ends bit. And so we can choose to do that and it will untrim that whole region. If you wanted to actually move this whole sequence, I'm not exactly sure if you could move the whole alignment, but if you wanted to correct any of these nucleotides, like that's getting called as an N, but I actually think that that is a T, I could replace that and change that actually within the nucleotide trace there.
And so we can either kind of move that, maybe you could add in if you wanted to add in some gaps or anything like that there too. So if I wanted to say, delete this, I could delete that chunk there and maybe add in any spaces or gaps, and that might be a way to move it along, but it will automatically determine the region where it's mapping correctly. If you're seeing that it's not mapping correctly, let us know.
So that would be, that would be weird, but yeah, basically we'll go through and actually try and find where the best match is, but we can always edit either the backbone sequence or any of our Sanger sequences there as well. I think that hopefully that answers your question. If not, let me know.
I want to be mindful of folks' time. We did make it to the full hour. So feel free to hop off if you need to run and we'll put just be closing this shortly, but if you have any final quick ones for Evan, feel free to shout out.
Hi, Evan. Thanks for answering my last question. So just what I wanted to ask was, so I've got like mutant sequences where I've deleted like three or four amino acids, so about nine or 12 nucleotides.
And then when I try to align them with the reference sequence, I see the 12 nucleotides missing, but they're like one off because SnapGenie is automatically aligning it with sort of the next nucleotide, which is the same. So it's like one off, the deleted region. So I just want to move the deleted region one nucleotide to the left, align it.
Right. Okay. I got you.
So if we have this sequence, let me... Yeah. Yeah. If you had the original sequence and you had a big deletion here or a smaller deletion.
Yeah. How would you then move that to make sure that it matches correctly? Let's see here. Yeah.
I think you would probably want to start to add in gaps within there so we can actually type directly within the sequence here. So we pop this open and again, if the folks need to leave, welcome to leave. But if we've got an alignment there, and I think I might have missed one where that gap is supposed to be. But if say you needed to move this, could we add, for example, that G on the left, I just want to move that one, and if you type to the right, yeah, so, oh, yeah, if you wanted to move that guy, so, dash, dash, you know, I'm not exactly sure if that's, if that is entirely possible to actually move that. I might have to look, I might have to look into that, how to actually move individual pieces of an alignment.
I will, let's see, let me, let me find your name here, and I can try and get back to you. Let's see, what was your name again, sorry, who am I talking to right now? Oh, Kalinda. Perfect.
Perfect. Great. Thank you.
Thank you. Yeah, I'll follow up with you and see if we can do that. Thank you.
Yeah, and I understand that Jessica probably has to go and close this session, but if anybody else has any other questions, reach out to the Snapgene team, and we're always happy to help. Great. Perfect.
Good to meet everybody. Nice to meet you again, and thanks, everybody, for coming until next time. Cheers.
Perfect. Thanks, everybody. Bye.
We work to ensure that you have the right tools from high-performance systems to optimized workflows to drive your projects forward and achieve groundbreaking results. The RCS team offers a diverse portfolio of services to support your research, and we'll put our URL in the chat. If you're interested, you can visit our website.
User training can support our key components of facilitating effective use of our resources and services, and today's session is designed to address that need by offering valuable insights from experts in the field. Feel free to ask questions, share your experiences, and make the most of the expert advice available today. I would like to quickly recognize Jessica Eaton, who is a research analyst on the RCS team and the organizer of today's workshop, and I'll pass the floor to Jessica, who will make a few announcements and introduce our speaker.
Jessica, the floor is yours.
All right, thanks, Axinia. Yeah, just a few housekeeping things, folks.
So you may recognize my name from the purchase and license distribution for Snapgene, but if you're not aware, one of our services is gathering everybody who uses Snapgene at Columbia together to get a bulk discount on the software. Normally, the licenses are like $295 a year, but if you work through us at CUIT, you can get it for about $135 a year, and we renegotiate that price each year. We also do a similar program for GraphPad Prism, if that's something that you're interested in.
One thing that is new this year is we have finally put all this information about discounted software together on a single page and how to buy it, and so I'll drop that web page in the chat, too, just so you can know the fastest way to getting your discounted license rather than just emailing me. All right. Also, as we mentioned, this session is being recorded.
It will be posted to our training page, and this is our planned agenda today. Just to check, is anyone here just getting started with Snapgene or doesn't even have Snapgene and is, like, considering it? Feel free to, like, raise your hand virtually or comment in the chat. If you can just do that to let Evan know if, like, a general very intro to the tool is needed, that would be good.
Looks like maybe everybody has some awareness. Also, I'll note that I did pull the topics that a few folks submitted with registration and put them at the bottom, so we're sure to get to them, but it's likely Evan will integrate these more organically earlier in the presentation, but those were some things that people had specifically asked for. And without further ado, I'll introduce our guest speaker, Dr. Evan Starr.
Evan has a Ph.D. from UC Berkeley in rhizosphere ecology, and he's worked as a soil carbon scientist and microbial ecologist. He currently works at Dotmatics, which is Snapgene's parent company, as a field scientist, and he's both a subject matter expert on Snapgene as well as a seasoned researcher. So if you have any presentations throughout the session, feel free to unmute yourself and ask, or you can put them in the chat, and then we'll bring them up.
Okay? And, Evan, it is yours. I will stop my share. Perfect.
Thank you, Jessica and Xenia. Thanks so much for inviting me. Really happy to talk to everyone.
We're going to go through Snapgene today, but as Jessica said, just unmute yourself, interrupt me with any questions. I try and keep these sessions as informal as possible and want to make sure you all get the most use out of it. If you don't want to unmute yourself or interrupt or anything like that, use the chat, and I'll try and keep an eye on that.
And if I don't see anything, folks are welcome to shout out and let me know if they do see anything there. So thanks for having me. Evan Starr, happy to talk about Snapgene today.
So Snapgene, as you all know, our molecular biology, cloning, general molecular biology toolbox. And so we're going to go through some of that, and I'm really happy to answer any questions, because it sounds like a lot of folks are very familiar with Snapgene. If anyone is not super familiar and is just getting started with Snapgene, or if you've got colleagues that are just getting started, we actually have a thing called the Snapgene Academy, and this is a great resource on our website for getting started.
And it's got videos. It's got written guides for all of the different common use cases within Snapgene. And it even has some, like, if you're ever teaching someone, it actually has, like, the science behind all of these different cloning tools and common molecular biology tools.
So Snapgene Academy is a great place to start to really get to learn how to use the program. What we currently have is Snapgene 7.2, and I'll introduce you to some features that have come out recently. We've got some new features that have come out, and what we also have coming out is in the near future.
We've got Snapgene 8.0, so a new version. We come out with new versions every year with some cool new features and introductions. So you're not obligated to update, but it is, like, safer and has all the fun new cool tools in it.
So Snapgene 8.0 is going to have a little bit of a UI redesign or a user interface redesign just to make it even easier to use. Some things are getting moved around, but we will show you where all of these things are getting moved around, and we'll try and make it as easy as possible to transition to this new user interface. There are going to be some new features included, like some of our homology annotations, and then one thing that is actually pretty exciting is that if people are familiar, we used to release a separate software called Snapgene Viewer.
That was basically the unlicensed, unpaid version of Snapgene that you could download, and you could basically open up files and view them, you know, like, do all of the kind of, like, viewing, but none of the editing with Snapgene files. So that's great if you've got a colleague who just wants to be able to view, say, a GenBank file, but doesn't want to go through any processes to get the full version of Snapgene. And so now that's all going to be bundled in one program.
So basically you can run Snapgene, the full program, without having a license, and you can still view everything, you just won't be able to necessarily do any of the operations that we're going to be talking about today. So that's some of the new stuff coming out in Snapgene 8.0. If you are interested in becoming a beta user or anything like that, you're always welcome to reach out to us. I was interested to hear people's thoughts and opinions about these types of redesigns especially.
Perfect. Just shout out again if anybody has any questions, but those are some of the new capabilities that we're releasing. I wanted to do a little bit of conversation about annotations, because that's really important, and there was also a question that came out with annotations.
And so what happens with Snapgene is we can, of course, open up our little folder here. And so this actually points to a folder on my computer. I'm using a Mac, so it's going to pop up right there.
And we've got that folder with all of these individual files in it. Sometimes you will get sent, for instance, like a sequence that's just a raw sequence of nucleotides, or you'll do some sequencing, anything like that, that you might want to get some annotations on. And so if we've ever got a new sequence, we can go ahead and annotate that directly.
So all we need to do is up here at the top is click our little New Sequence icon, or we can go through the File menu. In this case, it's going to be a DNA file. And so I'm just going to create a new DNA file.
And it's really easy to copy and paste that sequence in there. So what this is doing is it's copying and pasting my sequence in there. It's automatically creating a circular file and detecting some of my common features.
But if you've got a different topology, we can always change this around if you want. And then we'll give it a new little name, so New Plasmid there. And we can go through all of the techniques for adding in these new annotations.
So what you'll see is a bunch of annotations have popped up on this sequence automatically. Really common are plasmid types of features, right? Our restriction enzymes and our antibiotic resistance and our origin, all of that will appear. What we've got is a nice handy little drop-down menu where we can set our percent match.
So 96 is kind of what Snapgene thinks of as the standard. But we can always change this if you want to be either more strict or less strict with your annotations. And so if we come up to 100%, I think just about everything is going to be matching very closely.
But we can annotate all of those features on there. And if you didn't want to annotate any of them, we can uncheck them. And I'm just on my laptop screen, so you'll see that this stuff is kind of cramped.
If you're on a larger screen, it'll be a little bit easier to see. Or we can come into this more detailed view and see all of that metadata and the translation information that's coming along with that sequence. So really easy to just go ahead and annotate brand new sequences that we get brought in.
And then I'll talk briefly about adding in new custom features to annotate to and how to share those with colleagues. But does anybody have any questions about just that very basic, just annotating using those standard features? No? Perfect. So the other couple of options for annotations that we get are, if you ever wanted to, we can always select a region of DNA or RNA or protein.
Or we might have either one section or a couple of different sections. And all we need to do is go into Features and Add Feature. And so basically, all of the annotations in Snapseed are features.
And there are a lot of different ways of modifying, adding, removing all of these different features. So we can come up here into Add Feature. And we'll give it a name.
And I'm always really bad at naming things. I'm sorry, everybody. So we're going to call this a cool domain.
Great. So that's going to be the name of this feature. And then we can give it a type.
So there are a bunch of built-in common feature types, right? So common chunks of DNA or RNA or protein that we might see. But you can see that I've also added in some custom ones. For instance, like if I'm doing some antibody work, I might have my framework region or something like that.
And some of these are treated a little bit special. For instance, if you've got a CDS domain, that will be automatically translated in your annotation. But I'm just going to call this a miscellaneous feature because I don't want to get too complex.
If we wanted to, we can always split this feature or change the directionality of this or do any complex things with how we're adding this new feature. And we can add any metadata that we might want to add there as well. And again, this will all be carried on over to any new features that we annotate using this.
So easy to annotate a new feature like that. And as long as I save it, we will have this saved in there as our new domain. But the important thing is to be able to then re-find this in other sequences, right? So you'll probably have other sequences that you're working with and you want to find this on those.
So instead of manually going through this whole process, we can instead add this to our common features. So basically, we will have a whole database of these common features, and we can start to add in new sequences to our custom features. So now if I add this, then every time I run that previous detect those common features, this new domain will appear.
And I see that someone is off. Do you have a question? Can I have a question? Yeah, perfect. So there are some cases that I want to leave new feature nameless, but I think it's not possible in Snapchat or is it possible? Nameless? That's a good question.
I don't think we can keep this without a name. I mean, I tried. I couldn't manage to do it, but you have to enter something.
Right. You do. Okay.
But you would prefer to not have anything in there. Yeah, sometimes. Because sometimes I just highlight those different regions with the same color, with the same name.
There is no point giving a name, but it forces me to give a name all the time. Right, right, right. Yeah, that's a good, that's an interesting use case.
So part of my job is obviously to come out and teach you all, but also to collect information from the field about what would improve that. So that's a good idea is to be able to make features basically without names. So part of this is to teach you all, answer any questions.
If you do have any suggestions or anything like that, you guys are always welcome to reach out. One thing that you could do is instead of making, you said you've got multiple different sections all with that little chunk, you could highlight the whole thing basically, and then split it up into multiple different kind of sub-annotations. But I think even then, they'll probably have to have names with how we currently work this.
So we would have this be a large chunk of DNA, right? And then we can actually start to split this feature into whatever segments you want, and have this be basically whatever four or multiple different sections. And we can start to recolor some of these chunks here. This is a little bit more manual where you got to like move the numbers around, but that could be a good way to start to kind of highlight some of these chunks of DNA.
Thanks for the question. Perfect. So with those features, we talked about going into features and detecting those common features.
We can also add those common features. And then really important part of this is when we come into Browse Common Features, we can always import and export our standard features or those custom features. So you can see I'm very bad at naming these things, but we could always export all of our features.
And when we send this to a new colleague, they can import them, and then they will be annotating all of those features that you are working with as well. So that's one way to just kind of start to share annotations. It'll share all of that metadata, all of those annotation types, all of that kind of thing.
Perfect. Any questions about other questions about annotation of sequences? No. Great.
So, and I think that that addressed one of our questions, unless anybody doesn't have—unless someone has a follow-up. Setting parameters for identifying common features is basically being able to use that Detect Common Features tool and setting a different threshold match for these different features. So you can use that, and we can always set this to default.
And if you don't like any of these, we can always turn them off. And actually, here we can see we found a couple new features on this chunk there. Perfect.
So I was going to move into some cloning operations, if that works for everybody, unless anybody has any questions about annotations. Great. Along with the Snapgene Academy, we've got articles and videos for every different possible type of cloning operation, but they're all going to work pretty similarly.
So if you ever wanted to know more about any of those operations, it's all going to be under Actions. And if we come down to any different technique, you'll see a little link out to any of those videos. And so that's a great way to kind of learn about any of these different cloning operations.
So here's a very generic example of doing some Gibson Homology cloning. So all we need to do is open up our Backbone and come into Gibson Homology. In this case, we're just inserting one fragment, but if we wanted to, we could insert multiple fragments next to each other.
So I've got my Vector open, and I'm going to click Insert Fragment. And so this has been selected as my Vector. If I had clicked on the wrong thing, we can always choose a different Backbone or Vector from down here.
And then we're going to, just like in the lab, we're going to linearize this sequence however we want. We can either use restriction enzymes or outward-facing PCR primers. So whichever works for you.
In this case, if we wanted to graft this onto our GFP, there's a nice NCL1 site right here that we can work with. If you wanted to get deeper into the sequence view, we've also got all of those same options as when we're looking at that viewer, again, down in the little cloning operation. So that can get you really precise into where you might want to clone something.
So I've clicked my NCL1 site, and now we'll go into our Fragment tab. And so that's whatever we want to insert into here. And we can choose from either any open documents or anything within basically our computer, anything that you can have access to.
And so here we can come to this map view. If I just wanted to insert this gene and not the upstream and downstream stuff, I can just click on that gene so that it's highlighted, and now that will be basically what we'll use as our template for generating our PCR primers. All we need to do then is go into Product.
So we've got our Vector and our Fragment, and we choose Overlapping PCR Primers. We can, of course, set all of the different temperatures, the amount of overlap that we want. We can even regenerate upstream and downstream restriction enzyme sites if we wanted to.
So if we go ahead and run this, we can choose our primers there, and it will automatically generate them. If you ever wanted to, we can go back and forth between all this. So if you didn't like this end product or if you wanted to rename any of your primers, you can always do that as well.
So now all you need to do is save it. And so good naming conventions, always important. So name this something that will make sense for you.
But this will create a new file that's got that end product that we've now cloned this gene into. So go ahead and click Assemble, and now we've got this assembled.dna. Perfect. So some fun things here.
We can turn on coloring, so that will color something if it's been newly added into this vector. We can come down into our sequence view and get a little closer look at our sequence and see if we like where it's being cloned into and what is happening. You'll probably notice that I forgot to remove a stop codon, so you probably want to change that in here as well.
If we wanted to come down into primers as well, there's a different tab here for primers. And what this will show you is basically, in our case, our two different primers, where they're binding on our sequence and the melting temperature. And you'll see that this one actually has an off-target hit at a pretty high temperature.
So maybe we don't really need to worry about that, but that will call that out for you just in case. One of the newer features of SnapGene is we're actually being able to show the structure. So structures of small chunks of DNA or RNA.
So depending on if you want to work with CRISPR guide RNAs or tRNAs or primers, we can always click Show Structure and see a nice little structure of that sequence. We do a couple of different calculations of the structure, and we'll give you a bunch of stats down here. This is just for the monomer, so we can look for any hairpins.
But we can also look for homodimers within our sequences as well. So some fun, fun features that we've got now with SnapGene. We can click on this guy too and do the same thing and see if we've got any hairpins or anything like that.
And all of this can be exported as an image or a dot bracket or however you might want to export this. And we can always change any of the parameters down here. For instance, change our temperature.
And you'll see the temperature is listed up there at the top. So fun new feature. If you have any thoughts about new ways you want to see structures or different kinds of structural stuff, let us know.
That's now a capability that's built into SnapGene and something we can continue to expand on. One of my favorite parts, and people who use SnapGene will probably know about this, is the history view. So basically, when we do any cloning operation, all of the history of that cloning operation will be saved in this final file.
And so what this means is that we can either resurrect any original documents, or if you send this to someone else, they can open it and they will see basically all of the operations that have been done. And this can be exported as an image or as a text. And what I really like is if you're going to have something maybe synthesized, and so you don't want to actually do this PCR or something like that, we can just double-click on any mid-step and generate that file.
And you can see now it's already got those overlaps on there for us. This actually brings up an important point of documenting all of your different cloning operations or any of your different work that you're doing. So one thing that SnapGene actually has is an integration with LabArchives.
So SnapGene and LabArchives are both owned by Dotmatics, our parent company. So this is a really easy-to-use, really customizable ELN that lets you basically drag and drop documents into it. You can import all sorts of fun, cool widgets or anything like that to do all of your work within LabArchives.
And once you get it set up, it's also easy to basically work with SnapGene and LabArchives at the same time. So we can either open up files directly from our lab notebook, and so that's a great way to basically use your lab notebook as a repository for a bunch of different documents. And then it's important to know that when you do, for instance, a cloning operation or make any edits and you save that same document that you downloaded from LabArchives, it will then save that back up to LabArchives.
So that can be a really handy resource for documenting what you're doing or attempting to do. If anybody has any questions about that, reach out to us or the LabArchives team. We have resources for that.
If you ever need to contact the SnapGene team, you can always click Help and ask a question, report a bug, make a suggestion. So we're always happy to hear from everybody. I'm just going to butt in real quick and just let folks know.
I'll put this link in our recap email, but LabArchives is doing a webinar specifically on workflows for LabArchives and SnapGene on October 16th. So I'll send you the registration link. That's that bootcamp thing.
So yes, exactly. Yeah. Perfect.
Thanks, Jessica. And I think they're also doing some stuff with GraphPad Prism too. So GraphPad Prism and LabArchives work together as well.
Yeah. Great. Yeah.
So I, you know, lab notebooks are really important and everyone's going electronic. So yeah. Let us know how you like these integrations and if there's anything else you'd like to see too.
Yes. We can contact support. Are there any questions about cloning operations or anything that we've covered so far? Or the integration with LabArchives, if anybody wants to see that a little bit more.
I would like to see that a little bit more. Perfect. Perfect.
That sounds great. So basically what we can do is within SnapGene, all we need to do is go into preferences and we can set up our connection with LabArchives. And we'll send out, I can send Jessica an email that's got a bunch of different links to this that can be sent out to all of you guys.
So basically we can connect LabArchives with basically using your email address between SnapGene and LabArchives. And so that enables this exchange of files. And so now, for instance, I made that final product wherever that went.
I don't think I saved it. But if I wanted to save, for instance, this file back up, I did some operations that have been done, and I can either go into Snapgene and save to lab archives, and that will automatically pop that file back into lab archives, and that will go to whichever one of your lab notebooks that you're using. So you'll see here I'm saving to one of my lab notebooks and a specific page, and you can see those recreated right there. And so now if I save this back to that document, it will, oh I think I'm signed in as a different user, sorry about that, it will then be able to save that document back up there.
And the same thing is if we go into Snapgene, and instead of save, if we go into, um, if we go into open from lab archives, let's see if this works, I've got so many different accounts for all these things, and we can go into open. So what that will do is it will allow me to open up this file, so I've basically pulled something from my lab notebook, and this could be just a repository of a bunch of plasmids. Now if I made some kind of, you know, chain, I went in and just deleted a big chunk of DNA or something like that, and if I clicked and saved that, it would save back to lab archives.
And I think I've modified my permissions, so it's not letting me do that, but that's basically a way that you can start to work with these files back and forth with Snapgene and lab archives. And I'll send out an article on how to use those two together. Does that answer a little bit of your question? Maybe.
Okay. Oh, perfect. Perfect.
Yeah. And then within lab archives, it's basically like a really easy and customizable way to do a bunch of different, you know, all of your different ELN types of techniques. And then once we've got those files actually saved into our lab archives notebook, you'll see that it is a little document here, and if I click that, it will either download it, or if we come to a different one, we can actually view these within the lab archives notebook itself and actually see the, you know, all the different annotations and get a nice little view of those different documents.
Ah, there's that little eyeball viewer there. It was just cut off on my screen, but basically lab archives has basically that free viewer of Snapgene built directly into it. So if you import any GenBank files with annotations or Snapgene files, they will all bring along all of those annotations.
And so you can view those directly within your lab notebook. All right, perfect. Any other questions about cloning or anything like that before we move on? Yes, I have a question.
Because of my lower outdated version or not, so the cloning, my understanding in which I tried, if you have two restriction enzymes, you type in and you can automatically generate a final construct, right? So the question I have regarding the gene targeting CRE lockspeed technology we often use. So you have a two lockspeed site. Once you add the CRE, when you pop out the two lockspeed can add the gene automatically generate the final construct? That's not specific cloning, but it's a way how you actually manage the sequence from editing, right? Exactly.
Yeah, yeah. Snapgene. And so would you like, you would obviously like to be able to do that within Snapgene, basically replace those chunks within Snapgene, is that right? Exactly.
So what I did is I have to manually find out the way lockspeed are then take out and stick them together. But I hope that Snapgene has a place we can choose. This is a CRE.
And there's a Snapgene, we are automatically looking for where lockspeeds are. Then once you click on it, it automatically generate the excised allele. That is a great idea.
Yeah, that would be a good idea. I don't think we've got a built in, I think right now it would be a manual system, but that is something that would be a handy tool, especially more and more these days to add in. So I'll bring that to our developers.
I can never make any promises about what will be included in future versions, but I think that is a good idea. And so, yeah, yeah, yeah. Yeah, of course.
Thank you. And yeah, we'll, yes, I think that's a good idea. And I think I, yeah, I know what you're saying.
If you do have any other thoughts or if you want to add more details, you're always welcome to make a suggestion as well. And that's always for everybody really valued by our developers. Right.
Yeah. I mean, that's a good thought. Lockspeed, they are flipper like all other like genetic engineering, because people always using Snapgene to manage their pocket alleles.
So when we have flux allele, white type allele, we want to generate a knockout allele automatically rather than going to a nucleotide by nucleotide taking out. Right. So, so you Snapgene is a fantastic tool to do this if it's doable.
Yeah. Yeah, it is. Yeah.
Let me, let me also take a look and make sure we don't have some secret little way, secret little handy trick to do that too. So I will. Yeah.
Oh, sorry. One second. Thank you for all the comments.
Everybody really appreciate it. Perfect. Anything else, any other questions about cloning or different synthetic biology kinds of things that we want to talk about before we move into maybe some primers and some agarose gel kind of stuff as well? No.
Okay. Perfect. So primers, I think I've discussed this with folks as well, basically within Snapgene, just like with making our features, we can select a region and manually generate primers within our sequence.
You'll see that we've got that length and the melting temperature. And all we need to do is select that region and come into primers and add primer. So easy to add top or bottom strand, rename that primer with whatever we want.
Always good to add in a description. And then if we want to modify this, so if we want to make a mutagenic primer or add in any enzyme sites or different little tags or anything like that, we have those automatically in here for you. So we'll have the five prime end and the three prime end marked for you.
And you can always either type directly in here or you can use any of these insert kinds of things here as well. The same thing goes for doing stuff directly within. So if you wanted to either delete, you'll see that we've got this little icon there where we're deleting some nucleotides or we can add in more as well.
And so we can start to generate these primers and you'll see that all of our percent GC and our melting temperature and stuff will all be recalculated. So easy to add primers to our template DNA. Again, it will all have that metadata that's associated with it.
But a lot of times folks are storing their primers basically in Excel is what everybody that I talk to uses. We're eventually going to try and build up a database for primer design and primer storage to be able to like kind of centralize all of that information. But right now we're just relying on Excel like everybody else.
So basically if you've got a database of primers and you want to see if any of them match to your sequence, all we do is go into primers and import primers. And this can either be from a different snap gene file. So if we've got two different snap gene files, we can see if any of those primers on that snap gene file match to our new file or we can import these primers from a list.
And so there are a lot of different ways to denote this format. It can be in a CSV or a fast file, anything that you might want, even from a clipboard. And then we do have these little options.
So if you're like, hey, I've got a giant list of primers, but I only want to find unique binders, we can click that on. Or if we want to add a little bit of wiggle room, we can look for maybe not a perfect match for the whole primer, but add in maybe a little bit of mismatches there as well. So a number of different ways to match all of your primers, and we can add them all to our sequence.
Once we've got them all added, of course, we can always export our primers. So go into our little primers tab, and we can select all of them and come into primers and export selected primers. So if you wanted to export those to then go purchase them or anything, you can do that as well.
And we can choose which metadata we're going to include along with that. Perfect. So it's a little bit of the primer work.
You can see if we've got any mismatches or weird binding sites, you'll see that. And again, we can always double click and modify, rename, whatever we might want to do with those primers. With primer work and with restriction enzyme kind of stuff, we start to get into our agarose gel kind of work.
And so we can start to talk about that. So if we go into tools, we can go into simulate agarose gel, and that will bring up this new little tool. And so we can choose a variety of different files that we want to bring in.
We can bring in those ones. We can bring in all of these. We can bring in a bunch of different files, and we will generate a new gel file.
And from this gel file, we can select each of our different wells and choose which primers we want to use within this sequence to amplify that or which. So here we're amplifying with PCR, or we can cut with different restriction enzymes. So you can either find those or use these little buttons to annotate some different restriction enzymes.
So a number of different ways that we can start to simulate these agarose gels. And then really handy too is we can always duplicate wells. And so those will duplicate with those same settings.
So if you needed to change something, you can always do that there as well. Once I save this, we'll save it as basically a gel file for Snapgene that Snapgene can then open. But we can always export this as a gel image, export a fragment list, export the DNA, whatever we might want to do from that agarose gel.
And this is handy to save back to maybe your lab notebook. So yeah, lots of features for agarose gels. And then we do a lot of science behind actually working out the correct agarose percentage and adding in different ladders that you might want to use.
So we can choose a variety of different ladders from common distributors there as well. So some handy ways to start to verify your data. One question that did come in was also talking about multiple sequence alignments for primer design.
So so far we've just been doing single sequences for doing primer design and all of our work. But Snapgene does have tools for aligning sequences as well. So that's both taking our reference sequence and aligning a Sanger sequence to it or doing a multi-sequence homologous alignment.
And so we'll talk about that real briefly and then we'll open it up to some questions. Basically what we can do is we can select a variety of different, in this case these are DNA, but they could be RNA or protein sequences. And I've selected all of them and we can align these sequences.
And so one of these new features has come out where we can just automatically align all of these sequences. So that will pop through and we can view that alignment. We can modify this in whatever way.
Say if we want to compare everything to one sequence or compare it to a consensus sequence, change the coloring or view any of our annotations, we can do all of that. One thing that we can't do is generate primers directly on these alignments. And so that was a really good question because I think that would be a helpful thing.
But what we can do is once we've made an alignment, we can always export this consensus sequence. And so that's a great way to actually generate our consensus sequence. And we can open up this side panel and choose how we're generating this consensus sequence.
So if we want it to be more strict or less strict, we can change that percentage of the threshold of what we're calling a nucleotide. And then we can right-click and export our consensus sequence into a new document. And that would be a handy way to then generate, basically, design primers based on that consensus sequence because then we would know if we've got dashes or if we've got non-homologous sorts of regions within there.
So that was a very quick little tidbit on making consensus sequences from multi-sequence homologous alignments. But then you could, of course, use that consensus sequence to then design your primers. All right.
I've been talking for quite a long time, so I want to leave room for any questions that people have. So does anybody have any things that they want to cover, comments, anything like that? You're welcome to unmute yourself or type directly in the chat. And I'm sure whatever questions you all have would be really valuable for everyone else as well.
Well, as people think about their questions, there are a variety of different tools that we weren't able to talk about. And a lot of those are going to be on those websites. And we can look through these.
There are some articles that I can send out, too, for using some other common tools that people might want to use, like choosing alternative codons or maybe using BLAST from within Snapgene as well. Did someone unmute themselves? Is there a question there? I think it's just me. Or is that Jessica? Perfect.
Perfect. Well, I went real quick there at the end to leave room for questions. So if anybody does have anything that I have already covered and wants to know more about, you're welcome to shout that out as well.
Yeah, we'll hang around here if anybody wants to chat. And then just look for the follow-up email from Research Computing Services with the links that Evan and I have both been mentioning. But yes, thanks, everybody, for coming.
And thanks again to Dr. Starr for the overview. It's been helpful. Yeah, thanks for inviting me, of course.
I'll stick around for the last 10 minutes and answer any last-minute questions. And then if anybody does want to find, I've been mentioning a lot of tools and going pretty quick. And so one really handy technique for finding some of these tools within Snapgene is just doing directly within this search.
So if you're like, OK, I know I want to find non-cutters, but Evan didn't mention non-cutting enzymes. If you just search within here, it will tell you all of the different ways, like places that that comes up. And so for instance there, we've got that nice, funny little floating guy.
And we will see our non-cutters. Oh, great, we've got a question. Can you show us how to align DNA to a chromosome? Yeah, of course.
Would that be like a small chunk of DNA or a Sanger sequence or a NBLAST? Perfect. Oh, we've got so many questions. Awesome.
Yeah, so if we've got a chromosome, in this case, this is just a plasmid, but this will work exactly the same. So if we've got a plasmid and we want to align a Sanger sequence to it, all we need to do is go into actions. And here, or no, sorry, we will go into tools.
And we will align to reference DNA sequence. And so this is one of the ways that we can align multiple sequences where they're entirely homologous across the entire end. Or this align to reference sequence is where it will determine where one or more Sanger sequences match to our sequence.
And so all you need to do is import your full chromosome. And then we will come down here and choose any of our AB1 files to map to. And that will automatically determine the correct directionality and where it matches along that whole sequence.
So you'll see this view here that kind of gives you a global overview of where that sample is, sequence is. Or we can click this sequence view, and that's kind of the best part where we can then actually see these traces and where they match on our sequence. And so if we scroll along here, you will be able to see if there are any mismatches that appear.
And we can even use these little arrows to hop to any of those next mismatches that might have occurred. Once you've got that, there are a variety of different things that we can do, like replace any of those nucleotides. If you wanted to basically make a new document using what you have made your source of truth, we can do that.
We can add in more, you know, Sanger sequences. This is just one, but we can do multiple all at once. You just select them in that little tool.
Yeah, perfect. And I'll send a follow-up with that. That will also be saved in this little tab.
Can I ask another question? Yeah, yeah. It's more of a suggestion, probably. So I wonder if a SNAP gene could integrate with Ensembl for certain gene structure.
For example, if you want to import one of the gene genomic sequences with exons and introns, can SNAP gene automatically annotate the introns exons for us? That would be really cool with Ensembl. Yes, SNAP gene does not have kind of that capability in terms of integrating or like annotating. It'll annotate like those subdomains.
So if you download a gene that has intron exon kinds of domains within it, within that one feature or multiple features, it will then annotate them as they get brought along, but it won't necessarily be like intron exon aware, you know, where it could be like, oh, it would make sense like homology wise that this would be an intron, but really that would cause a, you know, frameshift mutation. And so it probably that intron is one further or a little bit further or something like that. So it's not going to be maybe amino acid and translation aware, but it can do homology based annotations in that way that we talked about annotate from custom database.
Yeah. I just wondering because most of the gene structure, intron exon sequence already will define the Ensembl. So if SNAP gene can automatically import those information and automatically annotate for the users, that would be really time-saving.
Yeah, that would be time-saving. Perfect. Well, I'll bring that to our product managers.
That's a good idea too. Okay. Awesome.
Thank you. Yeah, of course. Thank you for the questions.
There's another question about BLAST and one about moving. Yes. Perfect.
So for BLAST, what we can do is if we've got any sequence here, all it does is go into tools and this will blast just against NCBI. And so if we've selected a region here, we can blast the nucleotide database, the protein database, translated nucleotide database, or if we select a protein sequence, we can annotate or blast that sequence there as well. So when I click this, what it does is it opens up a nice new little window just directly within BLAST that we can run, and it will have that be named what we had that named originally.
So it's not necessarily running BLAST within SNAP gene. It's just a real handy way of popping that document out into BLAST. And then once we've run that, we can also then, if you export a GenBank file, you can then import that into SNAP gene.
So that was under tools and BLAST. And let's double, let's check if we've got a translated feature. So if we've got a, this is still in the DNA space, can we then, ooh, we can now, even though it's just DNA, genius, or SNAP gene knows that it should be translated.
So we've got our translation there. And so we can either blast the DNA or the amino acid sequences there as well. That's pretty handy.
I never thought about that. Sorry, just an aside. And then there was a previous question about being able to move the DNA, move the DNA along the sequence to change the alignment.
So once we've got our sequences aligned, there are a couple things we can do. If you have basically SNAP gene will automatically trim these sequences. So you'll see I'm able to drag along here and basically expose more.
And so what SNAP gene does is it automatically trims some sequences and that is all by default within this, this little hide ends bit. And so we can choose to do that and it will untrim that whole region. If you wanted to actually move this whole sequence, I'm not exactly sure if you could move the whole alignment, but if you wanted to correct any of these nucleotides, like that's getting called as an N, but I actually think that that is a T, I could replace that and change that actually within the nucleotide trace there.
And so we can either kind of move that, maybe you could add in if you wanted to add in some gaps or anything like that there too. So if I wanted to say, delete this, I could delete that chunk there and maybe add in any spaces or gaps, and that might be a way to move it along, but it will automatically determine the region where it's mapping correctly. If you're seeing that it's not mapping correctly, let us know.
So that would be, that would be weird, but yeah, basically we'll go through and actually try and find where the best match is, but we can always edit either the backbone sequence or any of our Sanger sequences there as well. I think that hopefully that answers your question. If not, let me know.
I want to be mindful of folks' time. We did make it to the full hour. So feel free to hop off if you need to run and we'll put just be closing this shortly, but if you have any final quick ones for Evan, feel free to shout out.
Hi, Evan. Thanks for answering my last question. So just what I wanted to ask was, so I've got like mutant sequences where I've deleted like three or four amino acids, so about nine or 12 nucleotides.
And then when I try to align them with the reference sequence, I see the 12 nucleotides missing, but they're like one off because SnapGenie is automatically aligning it with sort of the next nucleotide, which is the same. So it's like one off, the deleted region. So I just want to move the deleted region one nucleotide to the left, align it.
Right. Okay. I got you.
So if we have this sequence, let me... Yeah. Yeah. If you had the original sequence and you had a big deletion here or a smaller deletion.
Yeah. How would you then move that to make sure that it matches correctly? Let's see here. Yeah.
I think you would probably want to start to add in gaps within there so we can actually type directly within the sequence here. So we pop this open and again, if the folks need to leave, welcome to leave. But if we've got an alignment there, and I think I might have missed one where that gap is supposed to be. But if say you needed to move this, could we add, for example, that G on the left, I just want to move that one, and if you type to the right, yeah, so, oh, yeah, if you wanted to move that guy, so, dash, dash, you know, I'm not exactly sure if that's, if that is entirely possible to actually move that. I might have to look, I might have to look into that, how to actually move individual pieces of an alignment.
I will, let's see, let me, let me find your name here, and I can try and get back to you. Let's see, what was your name again, sorry, who am I talking to right now? Oh, Kalinda. Perfect.
Perfect. Great. Thank you.
Thank you. Yeah, I'll follow up with you and see if we can do that. Thank you.
Yeah, and I understand that Jessica probably has to go and close this session, but if anybody else has any other questions, reach out to the Snapgene team, and we're always happy to help. Great. Perfect.
Good to meet everybody. Nice to meet you again, and thanks, everybody, for coming until next time. Cheers.
Perfect. Thanks, everybody. Bye.