[Bioperl-l] UCSC database backend

Chris Fields 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  
> 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.

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  
> reasonable,
> 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.

> Sean
>
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Christopher Fields
Postdoctoral Researcher
Lab of Dr. Robert Switzer
Dept of Biochemistry
University of Illinois Urbana-Champaign





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