[BioC] problem with rat database

[James W. MacDonald]

Hi Alberto,

On 5/25/2011 5:35 AM, Alberto Goldoni wrote:
> Dear All,
> i'm working with a agilent rat microarry, what i would to know if
> there is a script or a package that starting from the GeneName
> "CB606456" it gives to me the Genomic location(strand)  for example
> chr 7:16261621-16262210 as you can do pasting the GeneName "CB606456"
> to the ensamble database.

That's not a gene name, as it points to an EST, which isn't AFAIK a 
gene. Instead it is an EST ID or some such thing.

The problem with the sort of query you want is that most of the 
available tools aren't as sophisticated as the Ensembl browser, which 
seamlessly queries lots of different databases when you paste something 
in the query window. If you want to do this sort of thing 
programmatically, you will have to know for sure what sort of inputs you 
are using, as you have to know which table to query.

Are all of the IDs you have similar to the one you supply? If so, you 
will need to figure out exactly what they are (Ensembl isn't 
particularly enlightening), and then maybe we can help you to do your 
query. If you have other IDs, like entrez gene or ensembl, that would be 
much better.

Best,

Jim



> this because i have hundred of gene names and i would know the genomic
> location in a automatic way.
>
> best regards
>
>
>
>

-- 
James W. MacDonald, M.S.
Biostatistician
Douglas Lab
University of Michigan
Department of Human Genetics
5912 Buhl
1241 E. Catherine St.
Ann Arbor MI 48109-5618
734-615-7826
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