Charging Station: Solving the Clump Finding Problem
Understand how to solve the clump finding problem in DNA sequences by sliding a window to detect frequent k-mers. Explore algorithm optimizations that update frequency arrays efficiently rather than recomputing them from scratch. This lesson teaches you how to implement and improve clump finding to analyze large genomic data sets more effectively.
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 ...