Table 1.
Recovery of known binding sites and motifs by GLECLUBS in E. coli K12 and B. subtilis
| Genome | Binding sites or motifs | RegulonDB/DBTBSa | Contained in inter-operonic sequencesb | Recovered by motif-finding tools | Recovered by the top clustersc | Final recovery rate |
|---|---|---|---|---|---|---|
| Escherichia coli K12 | Binding sites | 1642 | 1411 (86%) | 1316 (93%) | 1065 (81%) | 64.8% |
| Motifs | 125 | 122 (98%) | 119 (97%) | 112 (94%) | 89.6% | |
| Bacillus subtilis | Binding sites | 568 | 481 (85%) | 450 (94%) | 357 (79%) | 62.9% |
| Motifs | 99 | 98 (98%) | 98 (100%) | 86 (88%) | 86.9% |
aRedundant binding sites in RegulonDB and DBTBS are removed and binding sites for RNA genes are not considered in this study.
bThe percentage in a brace is the recovery rate at that step of the prediction pipeline based on the previous step.
cThe top 400 and 300 clusters predicted in E. coli K12 and B. subtilis, respectively.