[Biojava-l] BioJava for SNP analysis?

[Rick Byers]

Hi,
This probably seems silly compared to the important work professionals like
yourself do, but genetics is currently just a hobby of mine.  I'm mainly
interested in analyzing my 23andMe results (and those of my friends and
family) as a way to further my education in genetics and make it personally
concrete.  For example, there are some interesting population genetics
results in the literature around population structure which I'd like to
apply (and perhaps make available to the personal genetics community where
it makes sense).  This would include analysis methods like comparing
individuals to identify regions half identical-by-descent, finding runs of
extended homozygosity, and perhaps machine learning methods (HMM, etc.) for
classifying genome regions into population sub-groups.

But yes I'm also interested in dbSNP lookup and connection to other data
sources (like HapMap) in order to provide analysis of specific regions
beyond what the standard websites give you (eg. using LD to predict alleles
relevant to specific traits/disease from strongly correlated genotyped
SNPs).

Since BJ doesn't really have anything for this yet, I think I'll continue
building some tools on my own to better understand the constraints, and then
try to figure out if there is something I can contribute back to BJ.  I'm
definitely interested to hear if you start something in BJ3 though - I'm
happy to try to use it and help where I can.

Thanks!
Rick

On Tue, May 25, 2010 at 6:10 AM, Sylvain Foisy
<sylvain.foisy at diploide.net>wrote:

> Hi,
>
> What do you have in mind? Genetic data representation? Databse connections
> ,
> like fetching SNP from dbSNP? Specific analysis methods? My lab is also
> into
> SNP big time and I have been looking for some like-minded people to start
> some work on this in BJ3.
>
> Best regards
>
> Sylvain
>
> ===================================================================
>
>  Sylvain Foisy, Ph. D.
>  Consultant Bio-informatique / Bioinformatics
>  Diploide.net - TI pour la vie / IT for Life
>
>  Courriel: sylvain.foisy at diploide.net
>  Web: http://www.diploide.net
>  Tel: (514) 893-4363
> ===================================================================
>
>
>