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% |