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I am a statistician and I'd like to test my new method on biological data. For this I am looking for genotype data for a number of individuals. That is, I am looking for something like this:

                    | Individual 1 | Individual 2 | Individual 3 | Individual 4 | ....
Chromosome 1 SNP 1  | AA           | BA           | AB           | BB           |
Chromosome 1 SNP 2  | AB           | AA           | AB           | BA           |
Chromosome 2 SNP 1  | BB           | AB           | BB           | AB           |
etc.                    

I don't really care about the species. Ideally I'd like to have data for complex and less complex genotypes (different number of chromosomes and number of SNP's).

Are there any publicly available data sets like this? I have been searching the internet, but I can't find any.

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that's the stated purpose of the thousand genomes project.

the thousand genomes project has.. 1000 genomes.

its all downloadable.

http://www.1000genomes.org/

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How about the allele frequency database?

http://alfred.med.yale.edu/alfred/index.asp

One of the main problems with SNP databases is that there are a lot of them so you can get lost quickly. This sight gives some overview on the available resources:

http://www.humgen.nl/SNP_databases.html

Hope this helps.

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There is a vast amount of genotype data available at VectorBase's population biology browser, it is a database of insects which behave according to many mathematical assumptions - e.g. the non-overlapping discrete generations and homogeneous mating landscape.

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