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: