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Fig. 6 | BMC Bioinformatics

Fig. 6

From: General continuous-time Markov model of sequence evolution via insertions/deletions: local alignment probability computation

Fig. 6

Simulation analyses on absolute alignment frequencies. Each panel compares the predicted absolute frequency of each local homology structure (ordinate) against the number of times that it actually occurred in a simulated dataset (abscissa). The predicted absolute frequency was calculated using Eq. (SM-7.1) in Additional file 1. Note the logarithmic scaling for both axes, which tends to exaggerate sampling errors on the lower-left region in each panel. Panels a, b and c, respectively, show the results with the simulated sets 1A, 1B and set 1B after removing long gapped segments. The panels a-c are reformatted versions of panels A-C of Figure 29 of [48]

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