Some Hidden Messages are More Elusive than Others

Minimum Skew Problem from the previous lesson now provides us with an approximate location of ori at position 3923620 in E. coli.

In an attempt to confirm this hypothesis, let’s look for a hidden message representing a potential DnaA box near this location. Solving the Frequent Words Problem in a window of length 500 starting at position 3923620 (shown below) reveals no 9-mers (along with their reverse complements) that appear three or more times! Even if we’ve located ori in E. coli, it appears that we still haven’t found the DnaA boxes that jump-start replication in this bacterium.