
The A/J genome was sequenced as part of the Sanger Mouse Genomes Project and you can obtain a list of SNPs they have called in tab-delimited format.

http://www.sanger.ac.uk/resources/mouse/genomes/

The Mouse Phenome Database at JAX is also a great resource as they have merged SNPs from many projects and provide annotated lists.

http://phenome.jax.org/

- Ben

Benjamin L. King, M.S.
Staff Scientist
Mount Desert Island Biological Laboratory
Salisbury Cove, ME  04672

On Mar 30, 2011, at 9:52 AM, Cook, Malcolm wrote:

> 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@r-project.org 
>> [mailto:bioconductor-bounces@r-project.org] On Behalf Of Hervé Pagès
>> Sent: Tuesday, March 29, 2011 6:43 PM
>> To: sabrina.shao@gmail.com
>> Cc: bioconductor@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
>> 
>> E-mail: hpages@fhcrc.org
>> Phone:  (206) 667-5791
>> Fax:    (206) 667-1319
>> 
>> _______________________________________________
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>> 
> _______________________________________________
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