[Genome] PicTar miRNA predicted sites

[Blythe, Jason]

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
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> 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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