rasbhari: Optimizing Spaced Seeds for Database Searching, Read Mapping and Alignment-Free Sequence Comparison
Normalized overlap complexity (OC) of pattern sets depending on the number of iteration steps in our algorithm. The first two plots show how the OC is reduced in a single round of the hill-climbing algorithm for different parameters. For a set of m = 10 patterns of length ℓ = 14 and weight w = 8, the algorithm converges after around 3,000 iteration steps of hill-climbing (upper plot); for a set of m = 20 patterns of length ℓ = 44 and weight w = 14, it converges after around 80,000 steps (middle plot). The lower plot shows how the OC is improved if the hill-climbing algorithm is run multiple times and the best result of all runs is returned.