Part I: Finding specific types of prokaryotic sequences 1. Why is it relatively easy to find genes in bacterial genomes? 2. Go to the week 7 folder, select E.coli, then copy

the entire DNA sequence. These are the first 10,000 bp of the raw E.coli genomic DNA sequence that we are going to study using various DNA analysis programs. 3. Go to http://www.fruitfly.org/seq tools/promoter.html paste the sequence into the window, then select "Prokaryotic," "yes" for "include reverse strand?" and click "submit." • How many promoters does it find on the forward strand? • Where do the three highest-scoring promoters start and end? • How many promoters does it find on the reverse strand? • Where do the three highest-scoring promoters start and end? 5. Go to BPROM - Prediction of bacterial promoters (softberry.com) and click "help.” • How accurate is BPROM? • How far is it from most bacterial promoters to the protein coding sequences? 6. Return to BPROM - Prediction of bacterial promoters (softberry.com) paste the E. coli query into the window then click "process." 4. How many promoters does it find? 5. Where do the three highest-scoring promoters start and end? 6. How do these compare with the previous site?