[Genome] PicTar miRNA predicted sites

[Pauline Fujita]

Hello Jason,

The picTar miRNA track only exists on four assemblies:

C. elegans Mar. 2004 (ce2)
D. melanogaster Apr. 2004 (dm2)
Human May 2004 (hg17)
Mouse Aug. 2005 (mm7)

If you need picTar data for an assembly that is not on this list (i.e. 
hg18) you can download the hg17 picTar track, and then use the liftOver 
tool to translate the coordinates from hg17 to hg18. The liftOver tool 
can be found here:

    http://genome.ucsc.edu/cgi-bin/hgLiftOver

and instructions for using the liftOver tool can be found here:

    http://genome.ucsc.edu/goldenPath/help/hgTracksHelp.html#Convert

You can get the picTar files in one of two ways: via the downloads 
section, or through the table browser. The downloads section can be 
found here:

    http://hgdownload.cse.ucsc.edu/downloads.html

If you click on the "Annotation database" link for your assembly of 
interest it will take you to a page where the picTar files can be 
downloaded. They will be listed at the bottom - for hg17 these files are 
available:

picTarMiRNA4way.sql
picTarMiRNA4way.txt.gz
picTarMiRNA5way.sql
picTarMiRNA5way.txt.gz

To get this information via the Table Browser after selecting your 
assembly of interest select:

group: All Tables
database: (ie. hg17)
table: picTarMiRNA4Way or picTarMiRNA5Way
region: genome
output format: all fields from selected table

Then click on "get output". Hopefully this information was helpful and 
answers your question. If you have further questions or require 
clarification feel free to contact the mailing list at genome at soe.ucsc.edu.

Regards,

Pauline Fujita
UCSC Genome Bioinformatics Group
http://genome.ucsc.edu



Blythe, Jason wrote:
> Hello-
>  
> Is there a specific track to download the pictar versions of the miRNA sites? I am able to get the TargetScan ones, but I do not see a specific place for these bulk download. Thanks.
>  
> jason
>
> ________________________________
>
> From: UCSC Genome Browser Help Desk [mailto:genome at soe.ucsc.edu]
> Sent: Fri 3/28/2008 3:12 PM
> To: Blythe, Jason
> Cc: 'genome at soe.ucsc.edu'
> Subject: Re: [Genome] 28 species alignment
>
>
>
> Hello Jason,
>
>         You can download the data from the 28-way Conservation track here:
> http://hgdownload.cse.ucsc.edu/goldenPath/hg18/multiz28way/
>
>         And here is some information about how the track was created:
> http://genomewiki.cse.ucsc.edu/index.php/Conservation_Track
>
>         You can read about the details behind any track (description, methods, display,
> credits, references) by pressing on the 'mini-button' to the left of the actual
> track display, or by clicking on the hyperlinked track name in the track
> controls (below the display).
>
>
> Regards,
>
> ----------
> Ann Zweig
> UCSC Genome Bioinformatics Group
> http://genome.ucsc.edu <http://genome.ucsc.edu/> 
>
>
>
> Blythe, Jason wrote:
>   
>> Sorry I was probably very unclear. Basically what we want to do is use the browser to determine the 28-species alignment. But we want to be able to extract that info and do some comparisons programatically. I see that I think the browswer uses MULTIZ to do the algnments, but I could not find good documentations for the process that we want to go for.
>>
>> Thanks
>>
>> ________________________________
>>
>> From: UCSC Genome Browser Help Desk [mailto:genome at soe.ucsc.edu]
>> Sent: Thu 3/27/2008 5:59 PM
>> To: Blythe, Jason
>> Cc: 'genome at soe.ucsc.edu'
>> Subject: Re: [Genome] 28 species alignment
>>
>>
>>
>> Hello Jason,
>>
>>         I am unclear as to exactly what you are trying to do.  Do you want to know how
>> to display the 28-species alignment track alone in the genome browser?  How to
>> get the sequence for all 28 species for some areas of interest?  Or something
>> completely different?  Please reply to the list with more details and we will
>> try to help you find a solution.
>>
>>
>> Regards,
>>
>> ----------
>> Ann Zweig
>> UCSC Genome Bioinformatics Group
>> http://genome.ucsc.edu <http://genome.ucsc.edu/>  <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.
>>
>>
>> Blythe, Jason wrote:
>>     
>>> Hello-
>>>
>>> I was wondering if there is a way to display only the 28-species alignment in a separate browsing window? We are tring to grab the short alignments of predicted miR sites and see if there are any species specific substitutions. We only need to do a handful, but it would be nice to be able to do it automatically. Thank you for you help.
>>>
>>> jason
>>>
>>>
>>> _______________________________________________
>>> Genome maillist  -  Genome at soe.ucsc.edu
>>> http://www.soe.ucsc.edu/mailman/listinfo/genome
>>>       
>>
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>>
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>> Genome maillist  -  Genome at soe.ucsc.edu
>> http://www.soe.ucsc.edu/mailman/listinfo/genome
>>     
>
>
>   
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> Genome maillist  -  Genome at soe.ucsc.edu
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