Dear All,

Thanks a lot for your suggestions. I did try with biomaRt to get CHR and POS
info for SNPs. When I query dbSNP for a particular gene (Geneview report),
we do get useful information such as validation, function and protein
residue etc. for SNPs. Is it possible to get these information using
biomaRt? If so, could you please tell me where can I find info for
appropriate fields?

Thanks again.

Kind regards,
Sharon


On Mon, Oct 19, 2009 at 10:38 PM, <Steffen@stat.berkeley.edu> wrote:

> Also to note is that biomaRt indeed queries Ensembl for SNP queries and
> these SNPs are from dbSNP mapped to Ensembl.
>
> The latest release notes from Ensembl 56 state:
>
> Ensembl variation mart 56
>
>    * Removal of Ensembl Celera, TSC and HGVBase information
>    * Human now on dbSNP 130
>
>
> Cheers,
> Steffen
>
> > It may also be noteworthy that the SNPlocs.Hsapiens.dbSNP.20090506
> > package has location and allele information for build 130 dbSNP
> > entries. A substantial quantity of SNP-related metadata is present in
> > the pd.genomewidesnp.6 annotation package.
> >
> >  'Queries' to dbSNP of a more general nature could probably be
> > programmed using various web services support packages in R/bioc.  If
> > you describe a compelling use case, code might be written to solve it.
> >
> > On Mon, Oct 19, 2009 at 4:30 PM, Marc Carlson <mcarlson@fhcrc.org>
> wrote:
> >> Hi Sharon,
> >>
> >> It's not clear to me from your email what you intend to do, but I know
> >> that some dbSNP data is available as a UCSC track and should therefore
> >> be obtainable by using the rtracklayer package.
> >>
> >>  Marc
> >>
> >>
> >> Sharon wrote:
> >>> Dear All,
> >>>
> >>> Is there any tool in Bioconductor to query dbSNP? I know that (correct
> >>> me,
> >>> if I am wrong) biomaRt is primarily for Ensemble.
> >>>
> >>> Thanks in advance.
> >>>
> >>> Kind regards,
> >>> Sharon.
> >>>
> >>>       [[alternative HTML version deleted]]
> >>>
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> >>>
> >>
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> >
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