[Genome] Queyring the repeat tables in dm2 mysql database

[Cook, Malcolm]

In dm2, I understand that to directly query the mysql database for
overlapping repeats to a given region, I need to contrive the query the
table named after the chromosome, i.e. 

	SELECT repName, repClass \
	FROM chr2R_rmsk 
	AND genoStart <= ? 
	AND genoEnd >= ? 

Am I correct that there is no way to query a single table, passing the
chromosome as a parameter, to achieve the same effect?

Thanks!

Malcolm Cook
Stowers Institute for Medical Research - Kansas City, Missouri
  

> -----Original Message-----
> From: genome-bounces at soe.ucsc.edu 
> [mailto:genome-bounces at soe.ucsc.edu] On Behalf Of Hiram Clawson
> Sent: Tuesday, March 06, 2007 1:06 PM
> To: Bushel, Pierre (NIH/NIEHS) [E]
> Cc: genome at soe.ucsc.edu
> Subject: Re: [Genome] MySQL database of the genome browser
> 
> Good Morning Pierre:
> 
> You can also download directly the actual MySQL tables in their
> binary MySQL format directly into your database without any
> loading:
> 	ftp://hgdownload.cse.ucsc.edu/mysql/
> These files would be copied directly into your /var/mysql/ directory,
> or wherever it is that your MySQL keeps its data files.
> 
> This saves you the time of loading the files from their ASCII SQL
> representations.  Note, these files are MySQL version 4.0.27
> They will function in newer MySQL versions.
> 
> --Hiram
> 
> Bushel, Pierre (NIH/NIEHS) [E] wrote:
> > Yes thanks a lot.
> > 
> > Pierre
> > 
> > -----Original Message-----
> > From: Brooke Rhead [mailto:rhead at soe.ucsc.edu] 
> > Sent: Monday, March 05, 2007 7:16 PM
> > To: Bushel, Pierre (NIH/NIEHS) [E]
> > Cc: genome at soe.ucsc.edu
> > Subject: Re: [Genome] MySQL database of the genome browser
> > 
> > 
> > Hello Pierre,
> > 
> > The MySQL database dumps are available from our downloads page:
> > 
> > http://hgdownload.cse.ucsc.edu/downloads.html
> > 
> > Go to your assembly of interest and then click on the "Annotation 
> > database" link.
> > 
> > The tables are also available on our ftp server, here:
> > 
> > ftp://hgdownload.cse.ucsc.edu/goldenPath/
> > 
> > After choosing the assembly of interest, click on the "database"
> > directory.
> > 
> > I hope this information helps.  Please do not hesitate to 
> contact us 
> > again if you have further questions.
> > 
> > --
> > Brooke Rhead
> > UCSC Genome Bioinformatics Group
> > 
> > 
> > 
> > Bushel, Pierre (NIH/NIEHS) [E] wrote:
> >> Is the MySQL database of the genome browser still 
> available?  I would 
> >> need the sql commands to create the database and the files 
> as tables 
> >> to insert into the database.
> >>
> >> Thanks,
> >>
> >> Pierre R. Bushel, Ph.D.
> >> Head of Microarray and Genome Informatics
> >> Biostatistics Branch
> >> National Institute of Environmental Health Sciences
> >> P.O. Box 12233
> >> RTP, NC 27709
> >> (W) 919-316-4564
> >> (F) 919-316-4649
> >> bushel at niehs.nih.gov
> _______________________________________________
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>