Table 3.
Combinatory effects of different motif-finding tools and their outputs on the recovery of known binding sites and motifs
| Combination of the tools and the number of their outputs (in braces) | Total number of motifs returned | Number of binding sites recovered | Number of motifs recovered |
|---|---|---|---|
| ME(5)+BP(5)+CU(5)+MD(5)+MS(5)+CS(5) | 30 | 1145 | 117 |
| ME(5)+BP(5)+CU(5)+MD(5)+MS(5) | 25 | 1144 | 117 |
| ME(10)+BP(10)+CU(5)+MD(5)+MS(5) | 35 | 1284 | 118 |
| ME(10)+BP(10)+CU(10)+MD(10)+MS(10) | 50 | 1300 | 118 |
| ME(10)+BP(10)+CU(10)+MD(10)+MS(10)+CS(10) | 60 | 1301 | 118 |
| ME(10)+BP(10)+CU(10)+MD(5)+MS(5) | 40 | 1292 | 118 |
| ME(10)+BP(15)+CU(5)+MD(5)+MS(5) | 40 | 1305 | 118 |
| ME(15)+BP(10)+CU(5)+MD(5)+MS(5) | 40 | 1316 | 119 |
| ME(15)+BP(15)+CU(5)+MD(5)+MS(5) | 45 | 1333 | 119 |
| ME(15)+BP(20)+CU(5)+MD(5)+MS(5) | 50 | 1342 | 119 |
| ME(20)+BP(15)+CU(5)+MD(5)+MS(5) | 50 | 1345 | 119 |
| ME(20)+BP(20)+CU(5)+MD(5)+MS(5) | 55 | 1353 | 119 |
ME: MEME; BP: BioProspector; CU: CUBIC; MD: MDscan; MS: MotifSampler; CS: CONSENSUS. The combination shown in bold is adapted in our algorithm.