Tuesday, 4 October 2011

OpenHelix Blog non programmatic ways of obtaining information from a list of SNPs

Obtaining information about SNPs

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.

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