[Genome] Queyring the repeat tables in dm2 mysql database

[Kayla Smith]

Malcolm,

The rmsk table is split so mysql queries must have the chrom_ in the 
table name.  However, the Table Browser ("Tables" on the blue bar on the 
top of the main page) could be used, as it will query all the split 
tables together.  You would have to set up a filter to get the results 
that you want.

I hope this is helpful to you.  Please don't hesitate to contact us 
again if you require further assistance.

Kayla Smith
UCSC Genome Bioinformatics Group

Cook, Malcolm wrote:
> 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
>> _______________________________________________
>> Genome maillist  -  Genome at soe.ucsc.edu
>> http://www.soe.ucsc.edu/mailman/listinfo/genome
>>
> 
> _______________________________________________
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