Hello everyone. I am interested in looking at variants that occur within the promoter regions across selected strains of E.coli. So far, I have obtained a list of promoters (ref E.coli k12) from RegulonDB. But the information they provided on the promoter sequence and position is not quite clear to me as there are some random bases that appear in upper case. I don't know what these bases signify hence making computing promoter start and end site for a bed file tricky. I have written to authors of the RegulonDB database but have not gotten a response from them in over a week now. I was wondering if anyone is familiar with using this database and help shed more light on this. Alternatively, you can recommend other databases where I could obtain a list of promoter sequences in the E.col k12 genome. Thank you in advance for your help.
