Tag Archives: GeneSNPs

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:

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

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: SNPs on Protein Structure

The wealth of SNP data we are seeing these days is providing major insights into inheritance, population frequencies, effects on regulatory regions, splice sites and–of course–coding regions. Coding non-synonymous SNPs change the amino acid sequence of a protein. To get a sense of what that means on the protein structure you could use the GeneSNPs resource. We have a complete tutorial on GeneSNPs that you could watch. But to get a taste of how this data can be presented I’m going to show you a quick example of a SNP that changes an amino acid sequence on a protein structure. This is done with the PDBViewer tools at GeneSNPs. It requires MDL® Chime software for your browser. It is great to visualize the changes and think about what happens on your proteins of interest.