Downloading multiple queries from dbSNP?

Question

[Bioaln]

Hello. I've been recently trying to download a bunch of SNP, geneview results, for many gene queries. How should I do this, if I want my result to be in table form such as this example: http://www.ncbi.nlm.nih.gov/projects/SNP/snp_ref.cgi?geneId=4151

So, a table in let's say .csv of .table format. I'm trying to extract AA locations and SNP variations. Doing this for one gene by hand is possible, but I have hundreds of them.

Thanks for answer and good day

Answer 1

[Steven Lakin]

If you provide the first few lines from the file format you have and the file format you want, someone can probably write you a quick script to transform it. Also, list the operating system you are using.

[Bioaln]

I only have gene names, in one file. My result should look like: (this is just example line of course)

Chr.Position  mRNA pos.  dbSNP cluser id  Heterozygosity  Function  Alelle  AA       Codon pos.  AA pos.
43106520      380        rs747212786      0.000           missense  G       Glu [E]  1           50

So how do I get this table from gene name?

[Steven Lakin]

Well I have good news and bad news.

Good news: what you're looking to do is possible and there is a way for you to get started quickly.

Bad news: the solution that you're looking for is a bit more complicated than what dbSNP was built to handle in one step.

You'll have to search on your gene name, organism, and any other filters in dbSNP, then go to the "Display Settings" dropdown menu and select "dbSNP batch" under the Reports section. This will put all of the rsids into the dbSNP batch query, then enter your email, select an output format, and hit run.

Example query: BRCA1[All Fields] AND ("Homo sapiens"[Organism] AND snp[Snp_Class])

Returned 5,538 results

Here is more reading for similar questions: http://www.ncbi.nlm.nih.gov/books/NBK44466/

If you were good with APIs and coding, you could probably automate this through something like BioMart's API, but it would likely take more time to figure out how to do that than to just enter your hundreds of genes as described above. Hope this helps.

[Bioaln]

Thanks, this will certainly help. I will look into BioMart API tho.

[Steven Lakin]

If you are more inclined to go the coding route, take a look at this post from a while back; it mentions a few tools that might be useful: Dbsnp : Best Way To Obtain Data On Snps