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HGDP Selection Browser

Gene ExpressionBy Razib KhanNovember 10, 2008 11:02 PM


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You know what the Human Genome Diversity Project (HGDP) is implicitly, they're the list of populations you've seen in many human genetics papers already. Now the Pritchard lab has put up a nice browser to query the data in a manner analogous to Haplotter. One of the major improvements, aside from the fact that you're looking at 52 populations instead of 3, is that it uses GET to pass parameters instead of POST. That means I can link to the queries for KITLG and SLC24A5. Try it, it works! Under instructions it is laconically stated that:

Search using a sequence name, gene name, locus, or other landmark. The wildcard character * is allowed. To center on a location, click the ruler. Use the Scroll/Zoom buttons to change magnification and position.

Great! But Dan MacArthur has a massive post, Do It Yourself: searching for evolution's signature in 53 human populations which drags you up the learning curve:

I'm introducing Do It Yourself as a new and hopefully semi-regular section on Genetic Future. The aim is to provide readers with instructions on how to access online resources for sequence analysis - an activity traditionally restricted to researchers, but one that will no doubt become more common as more and more people begin to access and interpret their own genetic data.

Read the whole thing. Really. Link the whole thing. Really. Caveat: 650,000 SNPs from 968 individuals in over 50 populations is great, but obviously we'll know more when we fill in the "blank spots" on the HGDP map and increase the density.

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