In the course, we investigate DNA replication, and ask the question, where in the genome does DNA replication begin? We will see that we can answer this question for many bacteria using only some straightforward algorithms to look for hidden messages in the genome.
Course content
Where in the Genome Does DNA Replication Begin?
A Journey of a Thousand Miles. . .
Hidden Messages in the Replication Origin
Some Hidden Messages are More Surprising than Others
An Explosion of Hidden Messages
The Simplest Way to Replicate DNA
Asymmetry of Replication
Peculiar Statistics of the Forward and Reverse Half-Strands
Some Hidden Messages are More Elusive than Others
A Final Attempt at Finding DnaA Boxes in E. coli
Epilogue: Complications in ori Predictions
CS: The Frequency Array
CS: Converting Patterns to Numbers and Vice-Versa
CS: Finding Frequent Words by Sorting
CS: Solving the Clump Finding Problem
CS: Solving the Frequent Words with Mismatches Problem
CS: Generating the Neighborhood of a String
CS: Finding Frequent Words with Mismatches by Sorting
Detour: Big-O Notation
Detour: Probabilities of Patterns in a String
Detour: The Most Beautiful Experiment in Biology
Detour: Directionality of DNA Strands
Detour: The Towers of Hanoi
Detour: The Overlapping Words Paradox