Saturday, December 8, 2007

GBrowse SNPedia

It is now easy to overlay SNPedia on the Gbrowse databases. This means you can generate images like

(click for full)

which shows a cluster of snps around TCF7L2. The upper track identifies SNPedia snps. The the lower track identifies all snps present on the Illumina 550 microarray. All are hyperlinked to their SNPedia pages. If you click on the image above, you'll see the full image with the LD plot at the bottom. This allows you to determine how much two neighboring snps can say about each other.

To generate your own visit the hapmap of Chr10:114724078..114764077

At the very bottom of the page add these two 'remote annotation urls'
The snpedia file is a modest 300kbytes, but the single illumina chip is 58Mbytes!

Every snpedia rs# page now has a direct link to the hapmap site. Loading will take a while. Scenic spots along the genome include:

*click on hapmap
*set Scroll/Zoom=40kbp (upper right)

*click on hapmap
*set Scroll/Zoom=100kb (upper right)

I'm aware of a problem with rs3135506, but unable to explain it. Other times, snps listed in the snpedia files files aren't rendering onto the images. Other bugs probably remain. Your bug reports are always helpful.

Annotations will be updated approximately weekly, along with the fasta.

(click for full)