Table 4.
Pattern discovery at the level of binding sites
| Consensus/Patser | Dyad-analysis/sweeping | |||||
| Regulon | Sites/sites | 250/sites | 450/sites | Sites/sites | 250/sites | 450/sites |
| AraC | 100.00 | 8.33 | 8.33 | 58.33 | - | 41.67 |
| ArcA | 76.47 | 76.47 | 47.06 | 76.47 | - | 76.47 |
| ArgR | 75.00 | 58.33 | 58.33 | 100.00 | 16.67 | 50.00 |
| CRP | 90.53 | 87.37 | 88.42 | 66.32 | 46.32 | 47.37 |
| CysB | 100.00 | 42.86 | 28.57 | - | - | - |
| CytR | 100.00 | 12.50 | 12.50 | - | - | - |
| FIS | 55.56 | 66.67 | - | - | - | - |
| FNR | 93.10 | 65.52 | 51.72 | 58.62 | 41.38 | 41.38 |
| FadR | 83.33 | 50.00 | - | - | - | - |
| FruR | 100.00 | 14.29 | 71.43 | 71.43 | - | - |
| Fur | 100.00 | 66.67 | 11.11 | 77.78 | - | - |
| GlpR | 60.00 | 40.00 | 40.00 | 80.00 | 33.33 | 46.67 |
| IHF | 72.22 | 66.67 | 22.22 | 50.00 | - | - |
| LexA | 100.00 | 88.89 | 88.89 | 100.00 | 100.00 | 100.00 |
| Lrp | 78.95 | 47.37 | 26.32 | 36.84 | - | - |
| MalT | 66.67 | 22.22 | 22.22 | 55.56 | 44.44 | 77.78 |
| NR_I | 77.78 | 55.56 | 55.56 | 77.78 | 77.78 | 77.78 |
| NagC | 57.14 | 14.29 | 14.29 | - | - | 28.57 |
| NarL | 75.00 | 35.00 | 15.00 | 55.00 | - | - |
| OmpR | 71.43 | - | 7.14 | 42.86 | - | - |
| OxyR | 75.00 | 25.00 | - | - | - | - |
| PhoB | 71.43 | 57.14 | 57.14 | 71.43 | 71.43 | 42.86 |
| PurR | 92.86 | 85.71 | 78.57 | 92.86 | 78.57 | 85.71 |
| TrpR | 100.00 | 100.00 | 100.00 | 100.00 | 100.00 | 100.00 |
| TyrR | 86.67 | 73.33 | 66.67 | 53.33 | 46.67 | 60.00 |
| Average | 88.59 | 60.36 | 53.07 | 75.19 | 70.76 | 65.64 |
For each family, we show the results of applying Dyad-analysis/sweeping and Consensus/Patser to the problem of discovering binding sites. The results contain pattern discovery data similar to those in Table 3, but this time counting the number of binding sites found per total number of sites. Again, only dyads extracted from max ROMs are used. The names of columns are as described in Table 3.