Tag Archives: SeattleSNPs

Tip of the Week: F-SNP

fsnp_thumbThere are a lot of databases to search for to find SNP data, HapMap, dbSNP, SeattleSNPs, Genome Variation Server and many more. I’m going to add one more to your data mining arsenal, F-SNP. F-SNP (described more fully here in the 2008 NAR Database issue),

provides integrated information about the functional effects of SNPs obtained from 16 bioinformatics tools and databases. The functional effects are predicted and indicated at the splicing, transcriptional, translational, and post-translational level. As such, the F-SNP database helps identify and focus on SNPs with potential pathological effect to human health.

…as they say in the introduction. It looks to be a good first stop to find SNPs of functional relevance. The databases they pull from to get their information include several I’ve mentioned above and also the UCSC Genome database, Ensembl, SIFT and PolyPhen predictions and more. I’ve given a quick intro in the tip this week on how to get functional SNP information from F-SNP.

Tip of the Week: Free bioinformatics training materials

We wanted to take this “tip of the week” to introduce you to some of the materials that we have which are freely available for you to download and use in classes, seminars, or just for your own learning. OpenHelix creates training materials that include tutorial movies (animated + audio), slides with script, and exercises to reinforce concepts developed in the tutorials. Some of them are sponsored by the software provider, so we can make them freely available. We can even send you these great Quick Reference Cards that you can give out to students, or tape next to your computer, which will remind you of many of the features of the site. You can access them from our blog, or from our regular homepage. This tip of the week movie introduces you to how to access these materials.

Sponsored Genomics Resource Tutorials, available again

Our server went down last week and the host provider had to move our server. The settings weren’t completely corrected, so if you have attempted to view the free tutorials and training materials this week, you might have had problems doing so.

We have fixed that problem and those links now work. Please visit our tutorials!

As a reminder, here are the tutorials that are sponsored by providers and free to the user:

GeneSNPs
sponsored by the National Institute of Environmental Health Sciences (NIEHS)

Genome Variation Server (GVS)
sponsored by the National Heart, Lung, and Blood Institute (NHLBI) and the University of Washington

Integrated Microbial Genomes (IMG)
sponsored by the Joint Genome Institute

SeattleSNPs
sponsored by the National Heart, Lung, and Blood Institute (NHLBI) and the University of Washington

UCSC Genome Browser (Intro and Advanced Topics)
sponsored by the University of California Santa Cruz Bioinformatics Group

VISTA Comparative Genomics Tools
sponsored by Lawrence Berkeley National Laboratory

Tip of the Week: Visualizing Genotypes

SeattleSNPs genotypeAnd maybe it will help you visualize peace too :). There are several sites and software programs (Haploview and GVS are two) that will help you do visual genotype, we are going to show you one here that is simple to use at SeattleSNPs. This tip will show you how to access SeattleSNPs VG2 software and quickly visualize SNP allele genotype data for a gene, either your own data or that from the SeattleSNPs project.

SNPedia on the HapMap GBrowser

SNPs are hot. Everywhere we go for training people want to see SNPs. SNPs from many sources. And we know a lot of places to find them. Although everything gets in to dbSNP, of course, sometimes it helps to look at subsets of SNPs that were the focus of special projects. For example, the genes and SNPs from WashU in the SeattleSNPs project are focused on inflammation. If your genes are on their list, you are golden–you can look at the gene of interest in deep detail. Same for the NIEHS SNPs–those genes and SNPs are environmentally influenced.

Other projects are broader. Of course, the HapMap project identified millions of SNPs in various populations. And they did this genome-wide. The HapMap folks created a browser to focus on their data–but viewed on the official genomic sequence. That browser is based on the GBrowse software, which many people have used to create views of their favorite genomes and data.

Sometimes you can take the SNPs from one project, and load them onto another place to look at them. In the case of SeattleSNPs, you can find any gene page and click to load those SNPs as custom tracks on to the UCSC Genome Browser by clicking the “Golden Path” links in the middle of the page.

I was just looking today at another source of SNP data that you can load into a viewer. SNPedia is a resource that collects SNP information. I just found out today on the SNPedia blog that you can view those SNPs right on the HapMap browser–it is so easy! There are 2 URLs for the SNPedia data (http://www.snpedia.com/files/gbrowse/snpedia and http://www.snpedia.com/files/gbrowse/microarrays, you can see more info about them on their blog). All you have to do is:

  • go to the HapMap browser (sample location from the SNPedia blog)
  • go down to the very bottom of the HapMap page
  • paste each of those SNPedia URLs in the “Add remote annotations:” section one at a time. Click the Update URLs button each time.
  • and the data gets loaded from SNPedia right on to the HapMap browser.

So you get the genomic context, the HapMap context, and the SNPedia data too. I clicked one of the ones in this view (rs7901695) and it took me back to the SNPedia page for that SNP–which links back to a GeneSherpas blog post. Isn’t it amazing what you can learn from blogs?