Tag Archives: mydomains

Video Tip of the Week: FancyGene for quick accurate diagrams

We offer a lot of training on some complex tools with huge volumes of data and features that researchers need to explore genomic regions of interest, or pathways important to their work, and more. But there are plenty of times when what a researcher needs is a simpler solution to solve an immediate smaller problem: generating diagrams to explain their own research. It might be needed for a lab meeting, or a seminar, or a grant proposal. But it’s still something that really can matter. And you may be trying to represent new data that’s not in a current database, and to highlight specific features that are important to the point you need to make.

Today we highlight another tool of this sort that we learned about on BioStars: FancyGene. It’s a handy web-based tool that can help you to illustrate features of interest on a sequence, that you can customize and output in various ways to suit your purpose.

The question on BioStar was from a person who needed to diagram 73 mutations on a gene with 60 exons. Zoiks! Imagine trying to hack that out in PowerPoint–right? But you can do that sort of thing with FancyGene. You don’t need to know how to program–you can create everything you want with just a little structure and syntax. Or if the data you want is in an existing resource, you can export the data from tools that give GTF (gene transfer format) output and load that right up. I’ll use an example of that in my tip today, starting with the UCSC Genome Browser to show you how that works.

You can look at their paper and their documentation for more features and guidance, such as:

FancyGene also accepts a simpler format, which is intended for sequences not yet added into the databases. In this format, each line contains the start and end points of the gene exons, while introns are computed automatically. If known, it is possible to add a label to define the direction of transcription, as well as information on UTRs.

And in the past we know we’ve had a lot of questions about how to represent domains, so I wanted to highlight that as well:

Information on domain architecture (domain name, start and end within the protein sequence) can be uploaded either manually by the user, or automatically by using the summary provided by public domain databases, such as SMART (Letunic et al., 2009) (http://smart.embl-heidelberg.de/) and PFAM (Finn et al., 2008) (http://pfam.sanger.ac.uk/). FancyGene automatically converts the amino acidic coordinates of the protein domain into nucleotide coordinates and superimposes the domain architecture starting from the first coding exon.

If you need to diagram some features on your favorite genes, check out FancyGene to see if it will offer you the things you’d like to see. Below I’ve also linked to a couple of other tools that do other types of simple and user-friendly but important visualizations of data.

Quick link to FancyGene: http://host13.bioinfo3.ifom-ieo-campus.it/fancygene/ Apparently has a new home: http://bio.ieo.eu/fancygene/

Previous tips on other tools of this nature, for simple graphical representations:

Tip of the Week: DomainDraw for quick motif diagrams

Tip of the Week: Draw your own domains (MyDomains)

Tip of the Week: WebLogo for representation of alignment/motifs

Tip of the Week: IceLogo for conserved sequence displays

Guidance on the UCSC Table Browser (free sponsored tutorial): http://www.openhelix.com/ucscadv

Reference:

Rambaldi, D., & Ciccarelli, F. (2009). FancyGene: dynamic visualization of gene structures and protein domain architectures on genomic loci Bioinformatics, 25 (17), 2281-2282 DOI: 10.1093/bioinformatics/btp381

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.