[Genome] random DNA sequence generator

[Sean Davis]

Sean Davis wrote:
> 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.
>   
And the URL would be useful:

http://main.g2.bx.psu.edu/

Sorry for the noise....

Sean