[Genome] (no subject)

[Ann Zweig]

Hello again, Phil,

	The table underlying this track is called miRNA.  You can find this out 
yourself by holding your mouse over the track control and looking at the 
URL at the bottom of your browser screen.  The end of the URL will have 
the name of the database table, in this case: g=miRNA.

	From the download sever, navigate to the organism and assembly, then 
follow the 'Annotation database' link.  The file is called miRNA.txt.gz.

Regards,

----------
Ann Zweig
UCSC Genome Bioinformatics Group
http://genome.ucsc.edu


	


Kapranov, Philipp wrote:
> Amy,
> 
> One more question. I am trying to load the track "C/D and H/ACA Box
> snoRNAs, scaRNAs, and microRNAs from Weber and Griffiths-Jones". Again,
> I am having hard time finding it in the annotations... Could you point
> me to the name of the file(s)?
> 
> Thanks,
> 
> Phil
> 
> -----Original Message-----
> From: Ann Zweig [mailto:ann at soe.ucsc.edu] 
> Sent: Friday, June 08, 2007 10:58 AM
> To: Kapranov, Philipp
> Cc: Kate Rosenbloom; genome at soe.ucsc.edu
> Subject: Re: [Genome] (no subject)
> 
> 
> Hello Phil,
> 
> 	I'm not sure exactly what you mean by "load annotations".  But,
> I can 
> tell you about the Repeat Masker track and tables and maybe, with that 
> information, it will answer your question.  If not, please don't 
> hesitate to write back to the genome mail list.
> 
> 	The Repeat Masker track was created by using Arian Smit's
> RepeatMasker 
> program, which screens DNA sequences for interspersed repeats and low 
> complexity DNA sequences. The program outputs a detailed annotation of 
> the repeats that are present in the query sequence, as well as a 
> modified version of the query sequence in which all the annotated 
> repeats have been masked. RepeatMasker uses the RepBase library of 
> repeats from the Genetic Information Research Institute (GIRI).
> 
> 	There are 10 classes of repeats:
>      * Short interspersed nuclear elements (SINE), which include ALUs
>      * Long interspersed nuclear elements (LINE)
>      * Long terminal repeat elements (LTR), which include retroposons
>      * DNA repeat elements (DNA)
>      * Simple repeats (micro-satellites)
>      * Low complexity repeats
>      * Satellite repeats
>      * RNA repeats (including RNA, tRNA, rRNA, snRNA, scRNA)
>      * Other repeats, which includes class RC (Rolling Circle)
>      * Unknown
> 
> 	The tables underlying the Repeat Masker track are in a
> per-chromosome 
> format -- e.g. chr1_rmsk.  You can download these tables from our 
> download server here:  http://hgdownload.cse.ucsc.edu/downloads.html 
>  From this page, choose your organism and under the assembly name follow
> 
> the 'Annotation database' link.  The database tables in a tab-delimited 
> format compressed with gzip are named chr1_rmsk.txt.gz, etc.
> 
> 	Alternatively, you can use the Table Browser tool ("Tables" in
> the blue 
> navigation bar across the top of the website) to extract information 
> from the tables directly.  Set up the Table Browser to use the rmsk 
> tables like so:
> 
> group = variation and repeats
> track = Repeat Masker
> table = rmsk (this will combine all of the per-chromosome rmsk tables)
> 
> Then use the filter button and set the repeat class to choose only RNA 
> repeats like so: repClass does match *RNA*  (* is a wildcard)
> 
> 	You can get the output in a file, on the screen, or in the
> Genome 
> Browser as a custom track.
> 
> 	I hope this is helpful to you and that you can now get the
> information 
> you need.
> 
> 
> Regards,
> 
> ----------
> Ann Zweig
> UCSC Genome Bioinformatics Group
> http://genome.ucsc.edu
> 
> Please feel free to search the Genome mailing list archives by visiting 
> our home page, clicking on "Contact Us", then typing a word or phrase 
> into the search box.  On that same page 
> (http://genome.ucsc.edu/contacts.html), you can subscribe to the Genome 
> mailing list.
> 
> 
> Kapranov, Philipp wrote:
>> Hi All,
>>
>> Is there a way I can load the annotations belonging to the RNA repeat 
>> class of the Repeat Masker? Or, alternatively, is there a way I could 
>> load the entire Repeat Masker annotations and parse them for the 
>> repeats of various classes?
>>
>> Thanks a lot,
>>
>> Phil
>>
>> Philipp Kapranov
>> Senior Scientist
>> Affymetrix, Inc.
>> 3420 Central Expressway
>> Santa Clara CA 95051
>> tel. 408-731-5739
>> fax 408-481-0422
>> e-mail: philipp_kapranov at affymetrix.com
>>
>> -----Original Message-----
>> From: Kate Rosenbloom [mailto:kate at soe.ucsc.edu]
>> Sent: Friday, June 08, 2007 10:23 AM
>> To: Kapranov, Philipp
>> Cc: Jim Kent
>> Subject: Re: 
>>
>>
>> Hi Phil,
>>
>> I'm not sure what you're referring to here...  Repeatmasker
>> elements annotated as belonging to an RNA repeat class ?   You'll
>> get a quick answer by directing your question (with a bit more detail)
> 
>> to our mailing list (genome at soe.ucsc.edu)!
>>
>>      Cheers,
>> 	Kate
>>
>> On Jun 8, 2007, at 9:50 AM, Kapranov, Philipp wrote:
>>
>>> Jim and Kate,
>>>
>>> Is there any way we could load the RNA repeated elements track from 
>>> your browser? I can not seem to find it in the downloads...
>>>
>>> Thanks,
>>>
>>> Phil
>>
>> _______________________________________________
>> Genome maillist  -  Genome at soe.ucsc.edu 
>> http://www.soe.ucsc.edu/mailman/listinfo/genome