[BioC] SNP retrieval between two mouse strains

[Cook, Malcolm]

I think you'll find it at JAX using the form: http://www.informatics.jax.org/faq/STRN_SNP.shtml 

If you need it in a special format, or programmatic access, they stored this in for in a Sybase relational database for which you can request ( http://www.informatics.jax.org/software.shtml#sql):
	privs to connect
	the database schema 
	assistance writing SQL to get out exactly what you need.  

If you go the SQL route, you will then want to access JAX from within R and you would probably use RODBC with FreeTDS based ODBC driver following http://www.unixodbc.org/doc/FreeTDS.html.  I've done all but the RODBC part and it works fine.

Cheers,

Malcolm Cook
Stowers Institute for Medical Research -  Bioinformatics
Kansas City, Missouri  USA
 
 

> -----Original Message-----
> From: bioconductor-bounces at r-project.org 
> [mailto:bioconductor-bounces at r-project.org] On Behalf Of Hervé Pagès
> Sent: Tuesday, March 29, 2011 6:43 PM
> To: sabrina.shao at gmail.com
> Cc: bioconductor at r-project.org
> Subject: Re: [BioC] SNP retrieval between two mouse strains
> 
> Hi Sabrina,
> 
> On 03/29/2011 03:08 PM, sabrina wrote:
> > Dear list:
> > Is there anyway that I can retrieve genome-wide snp differences 
> > between A/J and C57BL/6J mouse strains, using any of the 
> bioconductor packages?
> 
> I don't think Bioconductor has any annotation package 
> containing this information. Note that Bioconductor does not 
> "produce" annotations, but re-packages/curates existing ones 
> to make them more convenient to work with in the Bioconductor 
> environment.
> 
> In addition to those re-packaged annotations made available 
> thru hundreds of annotation packages, Bioconductor also 
> provides several convenient tools for querying external 
> resources like biomaRt (for querying Ensembl and other 
> BioMart services), rtracklayer for downloading tracks from 
> UCSC, and others...
> 
> So more importantly than whether or not the information you 
> are looking for is available thru Bioconductor is the 
> question of whether or not this information is available 
> somewhere? Do you know any external resource (Ensembl, UCSC, 
> HapMap, dbSNP, etc...) where this information can be found?
> 
> Note that the C57BL/6J strain is *the* reference genome for 
> Mouse (latest release is NCBI Build 37, also called mm9 by 
> the UCSC folks).
> 
> H.
> 
> 
> > Thanks!
> >
> > Sabrina
> >
> > _______________________________________________
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> 
> 
> --
> Hervé Pagès
> 
> Program in Computational Biology
> Division of Public Health Sciences
> Fred Hutchinson Cancer Research Center
> 1100 Fairview Ave. N, M2-B876
> P.O. Box 19024
> Seattle, WA 98109-1024
> 
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> 
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