SNPs analysis.

Feb 10, 2015 at 4:55 AM
Edited Feb 10, 2015 at 4:55 AM
I'm trying to figure out a way to find the "evolutionary hot-spots" in a particular pool of sequences. I know Bio .NET can read the snps, but how would I go about an efficient way of finding the so called "hot-spots" (where the most snps tend to occur withing all the sequences). Some kind of heuristic? Thanks of any help, and all the help already provided in other posts!
Marked as answer by rooper149 on 2/19/2015 at 7:39 PM
Developer
Apr 19, 2015 at 3:33 AM
Hi Rooper,

The forums here are mostly designed for asking about the framework, programming practices, etc., and not so much how to go about designing a particular research question.

As a first start though, I would use google scholar to examine other work that has looked for evolutionary hot spots, such as the PhyloP papers which use HMMs, or you could use simple metrics as a pairwise diversity. If you have a more specific idea of thing(s) you would like to try, feel free to ping back and we can see if it is in the library.

-N
Aug 26, 2016 at 10:39 AM
To better design association studies for complex traits in isolated populations it's important to understand how history and isolation moulded the genetic features of different communities, such as dynorphin.