The OpenHelix Blog » F-SNP

Obtaining information about SNPs

Trey — Tue, 27 Sep 2011 15:07:26 +0000

This question was a while back on BioStar, ways to get information about a list of SNPs. It got me to thinking, what are the various ways to obtain a file of information about a list of SNPs (I’m assuming no programming skills, web or other simple query)? The obvious way for me is the UCSC Table Browser. Our tutorial (free) has an exercise that does just that. The question, for a given gene find data about all the SNPs annotated for that region, is simply answered.

What other ways are there? Turns out there are quite a few, I’ve started to list them here. All these I’ve used “clock” in human as my query and pulled a list of information about the SNPS in that region. In no particular order:

UCSC Table Browser (many species): See (tutorial - free)
Genome Variation Server (GVS, human only): click “gene name” > select populations & parameters > select “display SNP summary” > add or remove columns of data needed. (tutorial – subscription)
Ensembl BioMart (many species): choose Database (Ensembl Variation) > choose dataset (homo sapiens dbSNP 132) > choose filter (chromosome and start/end base pair) > choose attributes (name, strand, etc). (tutorial- subscription)
Varietas (human): choose genes > type in gene name > click search (a video tip from the blog)
F-SNP (human): click search > choose “query by gene” > type in “clock” > submit (a video tip from the blog)
dbSNP of course (many species): choose SNP database > choose limits (chromosome & location) > click search (tutorial – subscription)
SNPVar (various): in the comments below, Glenn details how to obtain a list using this NCBI feature. More here about gettings SNPs in a gene at NCBI.

Which one you choose will depend on what you want (species? data?) or what format you need. My favorite is still the Table Browser, but that’s a personal preference.

Do you have databases or tools to pull down a list of SNPs and data in a gene? Please mention them in comments below. For our purposes for this list, let’s stick with web-interfaces or simple queries. They could be specialized by species, or by type (disease-related?) or by other specialization such as related by pathway. I’ll put them here in this list.

For sql query or programming interface, you might want to explore the link to Biostar above, there are a lot of answers there too for that!

Tip of the Week: PolyPhen

Trey — Wed, 19 Jan 2011 05:33:37 +0000

There are several methods that can be used to predict if a particular non-synonymous SNP is deleterious; SIFT and PolyPhen, among others. Which one to use will be up to the individual researcher and the strengths and weakness of the predictors, though the two mentioned do a pretty good job. Today’s tip will be on the web interface of PolyPhen 2 hosted at the Sunyaev lab*. Many tools and databases use PolyPhen to help predict the functional effect of a nonsynonymous SNP including PolyDoms, F-SNP (which I’ve done a tip on before), NIEHS SNPs and SeattleSNPs (which we have free tutorials on), SeattleSeq and more. Today’s tip will focus on simply using the web interface, but you can always download the program and integrate it as you see fit or use one of the databases. Along with SIFT, it’s arguably one of the most used predictors out there.

From an earlier help section describing PolyPhen:

PolyPhen (=Polymorphism Phenotyping) is an automatic tool for prediction of possible impact of an amino acid substitution on the structure and function of a human protein. This prediction is based on straightforward empirical rules which are applied to the sequence, phylogenetic and structural information characterizing the substitution

To learn more about how PolyPhen works, you can view that page, or you can read some of the references. Next tip I do (early February) will be on SIFT.

Tool you might not know: F-SNP

Trey — Mon, 15 Sep 2008 23:32:46 +0000

We go through the thousands of resources and databases available online in our search to do tutorials we found many that are great resources but for one or more reasons we don’t or can’t do a tutorial for. Yet they are great resources. So, we occasionally do “Tip of the Week” on some, but even those are not enough to at least touch on all the great resources out there, so occasionally I we are going to give a quick “shout out” to some of these resources occasionally.

So today it’s F-SNP.

F-SNP is a “collection of functional SNPs, specifically prioritized for disease association studies.”

F-SNP integrates information from 16 different databases and analysis sites such as PolyPhen, UCSC Genome Browser tracks, dbSNP, OMIM and others to provide a collection of functional SNPs that have potential effect on human disease and pathology.

Search is simple and can be done by SNP ID, gene name or disease. The database contains information about the SNPs integrated from the databases and links to them.

It’s a nice site to check out to get started.