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Table 2 Selection of bootstrap cutoff values for plant-specific HMM training sets. Each row shows the results of building a new HMM using 80 initial training sequences plus the number of supplementary bootstrap sequences shown. "Inclusion threshold" indicates minimum score of the bootstrap sequences using HMM80. Accuracy and coverage were determined using the same positive and negative test set for each HMM. Jack-knife (leave-one-out) testing for each HMM was performed against the same training set used in model construction.

From: Predicting N-terminal myristoylation sites in plant proteins

Model Name Threshold Cutoff Pattern length Number Bootstrap Sequences Inclusion Threshold Accuracy (TP+TN)/TOTAL Coverage TP/(TP+FN) ROC area Jack-knife Detection
HMM80 2.05 22 0 - 100.0% 100.0% 0.969 82.5%
HMM109 0.85 21 29 > 12.5 100.0% 100.0% 0.969 92.7%
HMM166 0.65 21 86 > 9.6 100.0% 100.0% 0.968 96.4%
HMM185 1.40 20 105 > 8.8 100.0% 100.0% 0.969 96.2%
HMM 266 0.55 19 186 > 5.8 100.0% 100.0% 0.973 98.5%
HMM319 1.35 20 239 > 4.4 99.6% 98.8% 0.969 97.5%
HMM366 2.80 18 286 > 3.1 99.2% 97.5% 0.969 91.0%
HMM428 0.50 17 348 > 2.0 98.5% 98.8% 0.968 97.0%