UniSNP database

There have been a bunch of tweets lately around the UniSNP database–so I thought I’d do a quick post to raise awareness of that. The mission of UniSNP stated on their homepage at NHGRI is:

UniSNP is a database of uniquely mapped SNPs from dbSNP (build 129) and HapMap (release 27), where differences in SNP positions and names have been resolved, insofar as possible. In addition, SNPs are annotated with various functional characteristics, based on overlap with tracks from the UCSC browser. For details, see [PUB CITATION].

Well, I went looking for a [PUB CITATION] in PubMed for this. I entered the text UniSNP. I got a bunch of results. But that’s because….

Your search for unisnp retrieved no results. However, a search for unison retrieved the following items.

Unison? Um. Ok.

Anyway: the bioinformatics folks seem interested in this resource. So maybe others will be as well. It does offer you the opportunity to look for unique SNPs, using the UCSC assembly hg18/NCBI36. You can search by regions, or by starting with a list of SNPs, It gives you a dozen ways to filter the SNPs for things that might be of interest to you (RefSeq transcript characteristics, HapMap-ness, VISTA enhancer regions, etc).

I would probably accomplish this with a UCSC Table Browser query myself. But if you haven’t had a chance to get familiar with how to use that yet, this form would be a quick way to get similar answers.

Quick links

UniSNP: http://research.nhgri.nih.gov/tools/unisnp/

UCSC Table Browser tutorial: http://openhelix.com//cgi/tutorialInfo.cgi?id=28

The Table Browser tutorial is freely available to everyone as UCSC sponsors that. It’s the same material that we use in our live workshops, with the slides, handouts, and exercises available for anyone to use.

Here’s the tweet that’s going around if you’d like to re-tweet; hat tip to Khader:

@kshameer: UniSNP: uniquely mapped SNPs from dbSNP (build 129) and HapMap (release 27) http://1.usa.gov/gE3Ou0 #genomics #bioinformatics