Method | Algorithm | Correct helix count | Correct helix locations | Correct N-terminal | FP helix | FN helix | Correct SP topology | Correct RE topology | Correct topology |
|---|
MEMSAT-SVM | SVM | 95% | 91% | 91% | 4% | 5% | 93% | 64% | 89% |
OCTOPUS | NN + HMM | 86% | 83% | 84% | 14% | 2% | 21% | 73% | 79% |
MEMSAT3 | NN | 84% | 76% | 84% | 8% | 8% | 57% | 64% | 76% |
ENSEMBLE | NN + HMM | 77% | 76% | 79% | 18% | 5% | 7% | 55% | 67% |
PHOBIUS | HMM | 75% | 76% | 79% | 9% | 16% | 93% | 36% | 63% |
HMMTOP | HMM | 77% | 76% | 78% | 18% | 6% | 29% | 64% | 63% |
PRODIV | HMM | 79% | 64% | 76% | 19% | 8% | 0% | 18% | 57% |
SVMTOP | SVM | 66% | 64% | 66% | 22% | 22% | 0% | 55% | 53% |
TMHMM | HMM | 75% | 68% | 72% | 14% | 20% | 29% | 55% | 53% |
PHDhtm | NN | 75% | 54% | 55% | 23% | 30% | 29% | 18% | 45% |
- Column 1: Method – Prediction method. Column 2: Algorithm – Underlying machine-learning algorithm. Column 3: Correct helix count – Fraction of sequences with the correct number of TM helices predicted. Column 4: Correct helix locations – Fraction of sequences with the correct number and locations of TM helices predicted. Column 5: Correct N-terminal – Fraction of sequences with the correct N-terminal location predicted. Column 6: FP helix – Fraction of sequences with at least one over predicted TM helix. Column 7: FN helix – Fraction of sequences with at least one under predicted TM helix. Column 8: Correct SP topology: Fraction of sequences that contain signal peptides that have correct overall topology predicted. Column 9: Correct RE topology: Fraction of sequences that contain re-entrant helices that have correct overall topology predicted. Column 10: Correct topology: Fraction of sequences that have correct overall topology predicted, requiring the correct number and location of TM helices and correct location of the N-terminal. TM helices must overlap their defined positions by at least 5 residues.
