Tip of the Week: DomainDraw for quick motif diagrams
Bioinformatics resources can be really complex–sometimes daunting, heavily loaded with crucial data, and provide amazing visualization of large data sets and various features of the underlying data. And other times, that’s way more than you need. Overkill. Like aiming an elephant gun at a mosquito.
A couple of times in the last week I was noticing that questioners at BioStar wanted something more simple to just illustrate a few features of their genes/proteins of interest in a slide or figure format. They didn’t want to do them in PowerPoint, because they wanted some specificity in the locations–not just something freehand–but the UCSC Genome Browser has way too many things for what they wanted to show, for example.
If you have a known protein, one of my favorite tools to show a domain diagram is SMART. If you go and call up a protein like the sample one they offer TEC_Human:
When you are using SMART not only do you get these great diagrams, but you can link to details of the domains, and so a whole bunch of searches, and more. It also gives you a nice numerical output of the domains, which I’ll show here because I’m going to use in the example:
But there may be times when you want to show a diagram like this, but customized for your work. Maybe you made this protein without the SH2 domain. Maybe you discovered a splice variant that lacks the BTK domain. Or you want to show several homologs that have the domains in slightly different places. There are plenty of reasons to want a figure like that.
Although there were multiple answers at BioStar to solve this, I wanted to focus on one of the cool answers that was provided. The answer that solved the problem for the questioner was DomainDraw.
DomainDraw has been around for a while, but I can see it being quite useful for a long time. It can also be used for any organism–or even any synthetic construction. You can create a more complex file, but for simple drawings you can just enter a few parameters and draw a little protein. Using the numbers I had for TEC above, I drew this:
It’s not quite as striking as the SMART one, but it gets the job done. And you could very quickly tweak it to have smaller pieces, or remove domains, or whatever you might want to do to illustrate features of interest among splice variants or related proteins.
I wish there were more simple problem-solving sort of apps like this. If anyone has other handy little items like this, let me know in the comments. We are always looking for new ones to highlight in our weekly tips!
Quick link to DomainDraw: http://domaindraw.imb.uq.edu.au/
Previous tip of MyDomains: http://blog.openhelix.eu/?p=679
OpenHelix Tutorial on SMART (subscription required)
BioStar questions related to this:
Fink JL, & Hamilton N (2007). DomainDraw: a macromolecular feature drawing program. In silico biology, 7 (2), 145-50 PMID: 17688439