[Bioperl-l] UCSC database backend
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
>> DAS or local flat files indexed by whatever means. Data at UCSC is
>> 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.
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