Tag Archives: Domains

Online chart tools

One of the biggest challenges in the era of big data is representing the material you want to explore. As with a lot of bioinformatics tools, there are some excellent strategies with a variety of software tools depending on what you want to display. Sometimes you need something with a little less overhead, though–for presentations, classes, or even lab meetings you might want something quick and handy to do an effective visualization. Sometimes you will want to use the heavy tools–but other times these will be sufficient.

Recently a former colleague (Steffen Schmidt–thanks!) pointed me to several useful tools for generating charts online. The first source he provided was a blog post called 22 Useful Online Chart & Graph Generators. You’ll find a number of choices there you could explore–and I noticed in the comments that other people offered further suggestions.

I’ll highlight another one that was recommended by Steffen that’s not on the list.  Gliffy looks like it offers a nice range of visualization types, and he’s had success with it before. There is a free version where you can do 5 diagrams (note: they are publicly visible under this free plan, which may not be the best thing for your unpublished data, but fine for lab meeting or blogging), and there are subscription version with further features that might be useful in lab/collaboration situations it seems.

You may need more specific visualization tools for other scientific purposes, of course. In the past we’ve talked about the UCSC Genome Graphs tool as a way to show genome-wide data on a chromosome view.  I know there are tools in R that people have used for things I’ve seen. One of them was a word cloud feature. (But you can also use other sites for that such as Wordle). One of our more popular posts over the years was this one about a collection of tools for Venn Diagrams that are sometimes more bio-data specific: I ♥ Venns. Drawing domains has been another popular feature we’ve done a couple of times, once with DomainDraw and also with MyDomains.  People have also really enjoyed using WebLogo and IceLogo that we’ve highlighted that make these kinds of representations:

One of the biggest challenges going forward, though, is visual representation of the huge volumes of data we are seeing. How do you show what you want from 1000 genomes? 10,000 genomes? And that’s just the beginning….

Anyway–I hope this tip can help you visualize a few more things useful to your work, as we continue to wrestle with larger questions of big and complex data visualizations. If you have other handy quick drawing tools, or other smaller tools that just do something you need, let us know, we’d love to have a look at them.

Tip of the Week: Draw your own domains

prosite_mydomain1.jpgThere are some amazingly complicated programs in bioinformatics that do everything from assembling your genome to analyzing its evolutionary relationships and then make breakfast for you. Well, ok, not so many of them do the breakfast part. But the range and functionality of these tools is really tremendous.

However–there are times when users have simple needs and just want a quick way to make a diagram or an illustration of biological features. The MyDomains tool at Prosite is one way to make a quick diagram of items you would like on a sequence of interest. You can choose domain shapes, colors, indicate intervals and flag sites.

I can see this being handy for seminars, exams, grants, or any other place you might need a little custom diagram to represent features on a sequence. We have a longer tutorial in our catalog about the many other terrific features of Prosite, but here’s a quick look at a simple tool to make quality domain diagrams come to life.

New Tutorial Suite on SMART (protein domain analysis)

Comprehensive Tutorial on the SMART Bioinformatics Resource enables researchers to quickly and effectively use invaluable resource.

January 11, 2008 (Seattle WA) OpenHelix today announced the availability of a tutorial suite on the SMART bioinformatics resource (http://smart.embl-heidelberg.de/). SMART, created by the Bork Lab at the European Molecular Biology Laboratory (EMBL), contains information on hundreds of domains, and provides extensive annotations, phylogenetic analyses, and links to relevant resources about the domains.The tutorial suite, available for single purchase or through a low-priced yearly subscription to all OpenHelix tutorials, contains a narrated, self-run, online tutorial, slides, handouts and exercises. With the tutorial, researchers can quickly learn to effectively use this resource that helps them understand the evolution of function within multi-domain proteins. SMART brings together several functions that a researcher would otherwise have to perform separately.The tutorial will teach users to:

  • perform various text and sequence searches
  • find proteins based on their domain architecture
  • browse for key information about the evolutionary history and relationships of domains of interest to your researchTo find out more about this and other tutorial suites visit www.openhelix.com.

About OpenHelix
OpenHelix, LLC, (www.openhelix.com) provides the genomics knowledge you need when you need it. OpenHelix currently provides online self-run tutorials and on-site training for institutions and companies on the most powerful and popular free, web based, publicly accessible bioinformatics resources. In addition, OpenHelix is contracted by resource providers to provide comprehensive, long-term training and outreach programs.