[Bioperl-l] UCSC database backend

Sean Davis sdavis2 at mail.nih.gov
Thu Aug 10 07:10:52 EDT 2006




On 8/10/06 6:38 AM, "Joel Martin" <j_martin at lbl.gov> wrote:

> Sendu Bala wrote:
>> Sean Davis wrote:
>>> On another point, the strength of UCSC is not in obtaining sequence, but in
>>> mapping to the genome.  I think getting actual sequence should be secondary
>>> here, if for no other reason than there are trivially easy ways of getting
>>> sequence information from elsewhere given an accession or ID.  There is
>>> simply too much information to be stored locally for most people and getting
>>> the data remotely from UCSC doesn't seem possible currently.
>> 
>> The work would certainly be highly valuable even if it didn't allow for
>> sequence retrieval, but from my own point of view my main interest was
>> exactly the retrieval of arbitrary bits of genomic sequence - for which
>> there is no accession or ID that can be used to query some other database.
> 
> piping in as a user, retrieving sequence based on chromosomal coordinates,
> or offsets from coordinates of an acceession/model is a large amount of what
> I use ucsc for.  I'm not using it enough to store all that data but it's a
> nicely straightforward place to ask 'give me genomic seq for transcript ABC
> and 2kb off either end.  I wouldn't know how to ask that at ncbi.

Thanks, Joel.  I think little "use cases" like this are important to hear
about.  

Sean



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