Question: Extracting promoter regions alignment
0
gravatar for prosvirov.k
3.7 years ago by
prosvirov.k0 wrote:

Greetings, everyone!

I`m trying to extract promoter regions alignment from UCSC Table Browser.  I can get promoter regions for any species using output format as "sequence", also I can get alignments of "CDS" I guess, using output as "CDS FASTA....". So my question is divided into two:
1) Can I possibly combine these two options to acquire alignments of promoter regions uptream of XXX nc?
2) If not, could I possibly use "define regions" option with promoters` coordinates in human genome to acquire alignments using "CDS FASTA...." option? If it`s possible, could you tell me where to get promoter coordinates? 
Thank you in advance for your answers/advice/tips!

ucsc open promoters table browser • 1.1k views
ADD COMMENTlink modified 3.7 years ago by Sam70 • written 3.7 years ago by prosvirov.k0
3
gravatar for Sam
3.7 years ago by
Sam70
United States
Sam70 wrote:

Promoter regions aren't stonely defined I believe. Essentially you would look at the TSS of a gene and then choose a region (~3k+/3k- ... promoter region definitions vary) from there and that would be considered your promoter region. You can do this on the UCSC Table Browser I think, if not you could definitely do it using a combination of the Table Browser and slopBed from bedtools.

ADD COMMENTlink modified 3.7 years ago • written 3.7 years ago by Sam70
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