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rasbhari: Optimizing Spaced Seeds for Database Searching, Read Mapping and Alignment-Free Sequence Comparison

Fig 4

overlap complexity of pattern sets in the hill-climbing algorithm.

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 = 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 = 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.

Fig 4

doi: https://doi.org/10.1371/journal.pcbi.1005107.g004