What’s The Answer? (1000 Genomes signatures)

BioStar is a site for asking, answering and discussing bioinformatics questions and issues. We are members of the community and find it very useful. Often questions and answers arise at BioStar that are germane to our readers (end users of genomics resources). Every Thursday we will be highlighting one of those items or discussions here in this thread. You can ask questions in this thread, or you can always join in at BioStar.

In addition to the discussion and question sections, Biostar also has a section that allows contributors to publicize their tools and workshops and stuff like that. It’s called “ads” but don’t let the make you squeamish. I don’t think I’ve seen anything for sale–it’s been used to merely highlight the availability of some database or training so far. Outreach to scientists is tricking–it can be perceived as icky, but we really need ways to tell people about the tools out there.

I’ve been meaning to mention this tool but some other topical things had come up in the meantime. But now I wanted to mention this. It’s a custom installation of a UCSC Genome Browser framework that offers new ways to look at variations from the 1000 Genomes project.

Ad: A database of Signatures of Selection in the 1000 Genomes dataset

The 1000 Genomes Selection Browser is a database of Signatures of Selection in the Human Genome, based on the 1000 Genomes Phase I data. It is freely accessible at http://hsb.upf.edu/

The browser, based on a custom UCSC Genome Browser installment, allows to easily navigate the genome and visualize regions that are candidate for having been involved in an event of selection in any of the African, European, or Asian populations. The data can also be easily downloaded for further analysis here.

Our browser includes a total of 17 tests for selection. For each test of selection, we provide a raw score, plus a ranked score which compares each position to the rest of the genome.

[long list of the tests with further details....]

Go have a look at the details and then go over to the 1000 Genomes Selection Browser and try it out. The paper that describes is is linked below.

Reference:

Pybus M., Dall’Olio G.M., Luisi P., Uzkudun M., Carreno-Torres A., Pavlidis P., Laayouni H., Bertranpetit J. & Engelken J. (2013). 1000 Genomes Selection Browser 1.0: a genome browser dedicated to signatures of natural selection in modern humans, Nucleic Acids Research, 42 (D1) D903-D909. DOI:

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