[Genome] random DNA sequence generator

[Sean Davis]

Brooke Rhead wrote:
> Hello Peter,
>
> We do not have a way of generating random regions using the Genome 
> Browser.  However, the 'encodeRegions' table might be helpful to you. 
> You can get to it in the Table Browser by selecting "group: ENCODE 
> Regions and Genes", "track: ENCODE Regions" and "table: encodeRegions". 
>   It will at least give you a starting point for generating random regions.
>
> Once you are able to get a suitable list of regions some other way, you 
> could upload the regions as a custom track.  (Information on custom 
> tracks is here: 
> http://genome.ucsc.edu/goldenPath/help/customTrack.html#ADD_CT ).  Then 
> you could download the sequences of these regions from the Table Browser 
> by selecting your custom track and choosing "output format: sequence".
>   
Hi, Pete.  I saw your question and thought I would point out a tool that 
you and folks here might find useful as a supplemental tool for the 
Table Browser.  It is based heavily on the data in the UCSC genome 
browser and is being developed and maintained at Penn State.  The Galaxy 
server there allows you to upload essentially a custom track and then it 
will generate random regions to "match" the regions in your custom 
track.  You can also choose to mask out intervals; in your case, you 
would want to mask all the non-encode regions. You can download the 
encode intervals, perform a complement on those regions (a function also 
available via the Galaxy server), and use the result for your mask.  
Finally, they allow you to grab the sequences of your random regions if 
you need them.  I haven't actually done this, so check on the details, 
but I think what I described should work.

Sean
--
Genetics Branch
NCI/CCR/NIH
Bethesda, MD
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