Table 2.
The performance of motif-finding tools on the recovery of known binding sites and motifs in E. coli K12
| Tools | Top 1 | Top 5 | Top 10 | Top 15 | Top 20 | Top 25 |
|---|---|---|---|---|---|---|
| MEME | 298/83 | 877/109 | 1134/115 | 1202/117 | 1233/117 | 1254/117 |
| BioProspector | 354/85 | 743/103 | 953/112 | 1056/112 | 1150/116 | 1181/116 |
| CUBIC | 242/75 | 563/98 | 791/108 | 905/109 | 999/111 | 1062/114 |
| MDscan | 355/82 | 552/96 | 634/99 | 684/102 | 758/107 | 793/109 |
| MotifSampler | 168/61 | 486/92 | 612/102 | 729/102 | 792/107 | 831/108 |
| Consensus | 168/63 | 186/68 | 200/74 | 210/76 | 214/76 | 220/76 |
| Total | 731/106 | 1145/117 | 1301/118 | 1355/119 | 1379/119 | 1389/119 |
A known binding site is considered being recovered if a half length of its sequence is identified (the first number); and a known motif is considered being recovered if more than 20% of its known binding sites are recovered.