Snp Data Mining

Question

[Andrea_Bio]

Hello

Are there any tools available that will collect all of the known SNPs for a particular organism?

I can see that Ensembl uses dbSNP for its variation data but there are a lot of variations for an organism that are not listed in dbSNP. Naturally I do not want to write a custom script to mine various data sources if something already exists that does the job.

Many thanks

[Khader Shameer]

If you could share your organism of interest, you may get more precise replies from the BioStar members.

[Andrea_Bio]

I was thinking of mouse or cow

Answer 1

[Jorge Amigo]

if you browse Ensembl's Biomart, you will see that you are able to select a database first (your interest would be Ensembl Variation 59), and then you are able to select a dataset. well, there is where you just have to select your organism, and you will see that there are some with dbSNP data, some without, and some with multiple data sources, so you are not restricted to dbSNP only.

[Andrea_Bio]

Hi, when i looked at the organism I was interested in, only dbSNP was available using the route you have suggested. I was wondering if there were any other tools that could mine other databases for SNP information

[Jorge Amigo]

what Ensembl has been doing for a long time now is to intelligently merge self-generated information with other relevant resources such as dbSNP. if the only database present on Ensembl for your organism is dbSNP and this doesn't suit your needs, I guess you will definitely have to find an appropriate data resource first, and then try to mine it through its own interface or through any other of much general purpose.

[Andrea_Bio]

I have compared the number of SNPs for cow in dnSNP and ensembl and the latter has more so it would seem ensembl is getting some SNP data from somewhere else although I can't find the source. If you use the genome browser and look at the variation sources there it lists dbSNP and and another suitably vague option called 'other'