[Bioperl-l] UCSC database backend

Joel Martin j_martin at lbl.gov
Thu Aug 10 06:38:39 EDT 2006


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.

Joel


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