[BioC] SNP retrieval between two mouse strains

[sabrina]

Hi, Malcolm:
Thanks for the information.
I have been to the first website as for SNP query, but it did not work 
because I have to specify a value for at least one of the following 
fields: chr. Marker range or gene symbol, and I am after the whole geneome

for the  SQL route, do I have to have SQL account if I use RODBC? I 
never used that, can you show me what I need in order to go that route? 
I am using windows. Thanks

Sabrina

On 3/30/2011 6:52 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 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
>>
>> E-mail: hpages at fhcrc.org
>> Phone:  (206) 667-5791
>> Fax:    (206) 667-1319
>>
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