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!
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.