Finding promoter regions in bacteria

Question

[genseq]

I'm writing a program to find the promoter regions in bacteria. I though that the simple idea of getting let's say 100 nucleotides before the coding sequence on the DNA and calculating the consensus would work (at least would show some pattern). But, apparently, it doesn't.

Let's say we've got E.coli genome and annotations from NCBI RefSeq. Next we scan through annotation to get positions of CDS and record 100 nucleotides before the CDS (actually, I include first 3 nucleotides of CDS, usually ATG). https://ibb.co/kErQfw

But I see nothing similar to the Pribnow box. What am I doing wrong?

Answer 1

[Asaf]

1. The CDS start is not the transcription start site. You can get the TSS from EcoCyc if you would like.

2. There is some variation in the distance between the -35/-10 and TSS so you'll need something like MEME to find the motifs, it won't pop up using strict alignment

   I suggest to look at Hawley & McClure from 1983, they did a beautiful work with much less than we have today.