[Bioperl-l] UCSC database backend

Sean Davis sdavis2 at mail.nih.gov
Thu Aug 10 11:43:19 EDT 2006




On 8/10/06 11:39 AM, "Chris Fields" <cjfields at uiuc.edu> wrote:

> 
> On Aug 10, 2006, at 9:37 AM, Sean Davis wrote:
> ...
>> 
>> For genomic information, that can be done relatively easily, either
>> using
>> DAS or local flat files indexed by whatever means.  Data at UCSC is
>> stored
>> relative to the genome, so this may be enough, as long as one does
>> not care
>> about having the "original" sequence that generated the alignment
>> that UCSC
>> is reporting.
> 
> The caveat being the location info (sequence, strand, coordinates)
> from the local UCSC database has to correspond to the requested
> remote sequence.  That shouldn't be a problem if a local UCSC
> installation is updated periodically.

The genome files are not updated at UCSC.  They use an assembly as the basis
of each database and those sequences do not change, so having a local mirror
of the genomic sequence is probably not necessary except for speed issues.

Sean



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