[Bioperl-l] UCSC database backend
cjfields at uiuc.edu
Thu Aug 10 11:39:34 EDT 2006
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.
DAS would definitely fit in here.
>> Would be relatively easy if the MySQL table contains information
>> about which flatfile is used; that I don't know. If not, maybe use
>> an .ini file to map the tables to flatfiles?
> I don't think maintaining an additional file of flatfiles is
> given the complexity of the system at UCSC, but it is certainly worth
> mentioning as a possibility.
Only reason to bring it up, actually, is as a last resort.
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