Table 1.
Summary of the results obtained using the six identification systems with respect to the four mammalian TFBMs (i.e. hER, mTcfcp2l1, hAR and hVDR) ‘DA’ represents disagreement (see ‘Existing algorithms and their parameter settings’ subsection). The detailed results that were identified by the six programs are shown in Table S17
| TF | SSR reductiona | MDscanb |
MEME |
BioProspector |
Weeder |
DME |
MODIC |
||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| Rank (Correlation coefficient) | Frequency | Rank (Correlation coefficient) | Frequency | Rank (Correlation coefficient) | Frequency | Rank (Correlation coefficient) | Frequency | Rank (Correlation coefficient) | Frequency | Rank (Correlation coefficient) | Frequency | ||
| hER | × | DA | – | DA | – | DA | – | 1 (0.8687) | 23 | DA | – | 1 (0.9835) | 247 |
| ○ | 2 (0.8691) | 584 | DA | – | DA | – | 1 (0.8687) | 23 | DA | – | 1 (0.9837) | 224 | |
| mTcfcp2l1 | × | 5 (0.8842) | 1100 | 1 (0.9182) | 3811 | 1 (0.9506) | 2622 | 1 (0.8741) | 125 | DA | – | 1 (0.9767) | 1322 |
| ○ | 1 (0.8951) | 917 | 1 (0.9184) | 2683 | 1 (0.9506) | 2297 | 1 (0.8819) | 103 | 1 (0.8034) | 242 | 1 (0.9712) | 1100 | |
| hAR | × | DA | – | DA | – | DA | – | DA | – | DA | – | 2 (0.8980) | 242 |
| ○ | 1 (0.8882) | 228 | DA | – | 5 (0.9157) | 440 | 1 (0.8158) | 12 | DA | – | 1 (0.8951) | 159 | |
| hVDR | × | DA | – | DA | – | DA | – | 1 (0.8613) | 16 | DA | – | 1 (0.8891) | 60 |
| ○ | DA | – | DA | – | DA | – | DA | – | DA | – | 5 (0.8244) | 31 | |
aSSR reduction was performed by using RepeatMasker.
bWith MDscan, the DNA fragments in the datasets were sorted in terms of the P-values.