Table 2.
Per-segment performance for TMH (transmembrane helices). *
| TMH (571/2936) | |||||
|---|---|---|---|---|---|
| Recall (%) | Precision (%) | Qok (%) | Qnum (%) | Qtop (%) | |
| TMbed | 88.7 ± 0.6 | 88.7 ± 0.7 | 62.4 ± 3.7 | 86.0 ± 2.3 | 96.4 ± 2.7 |
| DeepTMHMM | 80.0 ± 2.4 | 80.5 ± 2.4 | 46.2 ± 4.8 | 85.7 ± 3.5 | 96.3 ± 2.2 |
| TMSEG | 74.5 ± 2.4 | 77.1 ± 1.7 | 35.6 ± 2.4 | 69.9 ± 2.7 | 83.8 ± 4.7 |
| TOPCONS2 | 76.4 ± 1.5 | 78.4 ± 0.8 | 41.0 ± 3.1 | 74.4 ± 3.3 | 91.7 ± 3.1 |
| OCTOPUS | 71.6 ± 1.5 | 75.7 ± 1.4 | 36.0 ± 2.8 | 67.6 ± 3.4 | 87.5 ± 3.1 |
| Philius | 70.8 ± 2.2 | 73.7 ± 0.8 | 34.2 ± 3.7 | 66.9 ± 3.4 | 87.5 ± 2.9 |
| PolyPhobius | 76.0 ± 2.1 | 76.4 ± 1.1 | 40.3 ± 3.5 | 74.5 ± 2.8 | 86.8 ± 2.7 |
| SPOCTOPUS | 71.5 ± 1.2 | 75.8 ± 1.2 | 35.7 ± 3.3 | 67.4 ± 5.5 | 87.2 ± 3.4 |
| SCAMPI2 (MSA) | 72.3 ± 2.7 | 74.1 ± 1.5 | 33.5 ± 3.0 | 72.2 ± 4.5 | 90.6 ± 3.5 |
| CCTOP1 | 77.0 ± 1.7 | 79.4 ± 1.0 | 41.9 ± 3.6 | 82.6 ± 2.7 | 92.6 ± 2.6 |
| HMM-TM (MSA)2 | 73.3 ± 1.7 | 72.5 ± 1.2 | 33.5 ± 1.4 | 72.1 ± 3.0 | 88.3 ± 4.2 |
*Segment performance for transmembrane helix (TMH) prediction based on 571 alpha helical TMPs (α-TMP) with a total of 2936 TMHs. Recall, Precision, Qok, Qnum, and Qtop were averaged over the five independent cross-validation test sets; error margins given for the 95% confidence interval (1.96*standard error); bold: best values for each column; italics: differences statistically significant with over 95% confidence (only computed between best and 2nd best).
1Evaluation missing for one of 571 α-TMPs.
2Evaluation includes only 552 of the 571 α-TMPs due to runtime errors of the method.