Charging Station: Solving the Clump Finding Problem
Let’s have a look at the solutions to the clump finding problem.
We'll cover the following...
This lesson assumes that you’ve read Charging Station: The Frequency Array.
The pseudocode below slides a window of length L down Genome. After computing the frequency array for the current window, it identifies (L, t)-clumps simply by finding which k-mers occur at least t times within the window. To keep track of these clumps, our algorithm uses an array Clump of length 4 whose values are all initialized to zero. For each value of i between 0 and 4 ...