Tag Archives: graphics

Video Tip of the Week: NCBI Sequence Viewer PDF export

A couple of weeks back we did a workshop on the UCSC Genome Browser, and I was asked a question we see pretty frequently: Is there a way to export the browser view that you selected with specific tracks, filters, regions, etc? People may want to have a record of their customized view in a lab notebook, or use it for teaching, or in a seminar perhaps–or of course to publish your awesome observations in journals.

Most of the time I just take screen shots of what I need with a screen capture tool (my personal favorite is Snag-It from TechSmith). But there may be times you want something a bit heavier-duty. If you are going to do a poster, or submit it for publication, for example, you might want a nice PostScript version you can work with and edit further. At UCSC, the way to do that is with the “View” menu option here for PDF/PS:

Export the browser image to a file for further editing or use.

Export the browser image to a file for further editing or use.

When you get a file, you can take it down and use Adobe graphics tools if you have them, or free open-source one like InkScape. You can change the colors, delete stuff, add more annotations, etc.

So when I saw that there was a similar function with the NCBI‘s Sequence Viewer tool, I thought I should mention that as well. They have a nice and clear video that illustrates how to accomplish getting the image out of the Viewer and into a file.

To try this yourself on the sample file they showed, you can go to NC_000022.10 in the Nucleotide database. From that page, click the “Graphics” link as shown here:

Click the "Graphics" link on the page to open the Sequence Viewer.

Click the “Graphics” link on the page to open the Sequence Viewer.

After you get to the sequence viewer, follow the instructions just as it plays out in the YouTube video. It’s pretty straight-forward–just watch out to click the right menu for PDFs.

If you haven’t used the NCBI Sequence Viewer much, you should definitely check it out. There are some other helpful videos for more features as well. And another neat feature is that you can embed sequence viewer in your own web pages.

All of the genome browsers have different features and functions, and it’s nice to know that there are various strategies to accomplish tasks you might need to get done.

Quick links:

Sequence Viewer homepage http://www.ncbi.nlm.nih.gov/tools/sviewer/

Videos: http://www.ncbi.nlm.nih.gov/tools/sviewer/videos/

References:

Karolchik D., Barber G.P., Casper J., Clawson H., Cline M.S., Diekhans M., Dreszer T.R., Fujita P.A., Guruvadoo L. & Haeussler M. & (2013). The UCSC Genome Browser database: 2014 update, Nucleic Acids Research, 42 (D1) D764-D770. DOI:

Acland A., Agarwala R., Barrett T., Beck J., Benson D.A., Bollin C., Bolton E., Bryant S.H., Canese K. & Church D.M. & (2013). Database resources of the National Center for Biotechnology Information, Nucleic Acids Research, 42 (D1) D7-D17. DOI:

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.