Video Tip of the Week: NCBI Variation Viewer

The folks at NCBI recently hosted a webinar that covered a number of resources: GTR, ClinVar, and MedGen. It was a nice introduction to these resources using a case study of exploring information about a 9-year-old child who needed to get clearance for participation in sports. So they follow the course of some details about this kid across the different resources at NCBI to show what you could learn at the different sites.

I was hoping that recording would become available so that could be a triple-tip of the week, but I haven’t seen any announcements of it; I’ll keep an eye out and highlight it in the future if it does. Below I have also referenced a paper that covers some of the same ground as that webinar. But in the meantime they also recently added a new short video about the Variation Viewer that I found handy as well. So that will be this week’s video tip.

I particularly liked the way you can easily select an exon to focus on, with the little bubbles near the top. That wasn’t obvious to me at first.  People are often asking me for handy ways to focus in on the specifics of a single exon.

In addition to this video, I will also offer a screen-cap of one of the slides from the longer webinar that linked to related resources around NCBI. If you haven’t checked out these associated tools you will want to look at them as well. There are a lot of terrific tools available and they are always adding new useful features. Follow them on Twitter for announcements about their tools and trainings–that’s how I stay on top of the new items.

NCBI webinar sitesQuick links:

Variation Viewer: http://www.ncbi.nlm.nih.gov/variation/view/

MedGen: http://www.ncbi.nlm.nih.gov/medgen

GTR: http://www.ncbi.nlm.nih.gov/gtr/

ClinVar: http://www.ncbi.nlm.nih.gov/clinvar/

Reference:

Landrum M.J., G. R. Riley, W. Jang, W. S. Rubinstein, D. M. Church & D. R. Maglott (2014). ClinVar: public archive of relationships among sequence variation and human phenotype, Nucleic Acids Research, 42 (D1) D980-D985. DOI: http://dx.doi.org/10.1093/nar/gkt1113