Table 2 Benchmarking results
From: FITBAR: a web tool for the robust prediction of prokaryotic regulons
# | Position | Gene(s) | Sequence | Str. | FITBAR (this work) | Simulation | PRODORIC Virtual Footprint[15] | RSA Tools[13] | RegPredict[16] | ||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Entropy-CIS | Entropy-LMM | Log odds-CIS | Log odds-LMM | Entropy | Log-odds | PWM Score | Score | Score | |||||||||
Score | P-value | Score | P-value | Score | P-value | Score | P-value | ||||||||||
1 | 4538216 | nanC fimB | cataattctcatcatgaaatatg | R | 0.95026 | 0.01634 | 0.95026 | 4.6 E-09 | 0.81891 | 0.01012 | 0.81891 | 0.00006 | 2.0 E-07 | 0,00052 | 17.84 | - | - |
2 | 1819873 | chbB | cttaattatcttcgcgaattatt | L | 0.93979 | 0.01898 | 0.93979 | 7.5 E-09 | 0.83231 | 0.00710 | 0.83231 | 6.9 E-06 | 4.4 E-07 | 0,00035 | 17.59 | 1.0 | 5.58 |
3 | 707425 | chiP | gataattcgcgtcgcgaaaaata | R | 0.93979 | 0.01898 | 0.93979 | 2.8 E-08 | 0.71507 | 0.02168 | - | - | 4.4 E-07 | 0,01746 | 17.50 | 1.0 | 5.71 |
4 | 1899865 | yoaE manX | gatattttacctttcgaaatttc | R | 0.92147 | 0.02905 | 0.92147 | 1.1 E-07 | 0.80400 | 0.01257 | 0.80400 | 0.00008 | 1.3 E-06 | 0,00110 | 17.29 | 1.0 | 5.48 |
5 | 400463 | iraP ddlA | aataattacccacacaaaatata | L | 0.90052 | 0.04027 | 0.90052 | 8.1 E-07 | - | - | - | - | 3.5 E-06 | - | - | - | - |
6 | 1580605 | ydeN | cttatttctcttcgtaaaattac | L | 0.89921 | 0.04076 | 0.89921 | 6.6 E-07 | 0.84788 | 0.00414 | 0.84788 | 4.4 E-06 | 3.5 E-06 | 0,00015 | 16.85 | 1.0 | 5.53 |
7 | 3537939 | feoA | ggtaattcactattcgaattata | R | 0.89660 | 0.04179 | 0.89660 | 7.9 E-07 | 0.67381 | 0.03302 | - | - | 3.5 E-06 | 0,05546 | 16.85 | - | 5.15 |
8 | 703020 | nagB nagE | tttaatttgcgatacgaattaaa | R | 0.89660 | 0.04179 | 0.89660 | 4.9 E-07 | 0.69745 | 0.02567 | 0.69745 | 0.00198 | 3.5 E-06 | 0,02854 | 16.83 | 1.0 | 5.21 |
9 | 3086266 | galP | cttaattcacaataaaaaataac | R | 0.89267 | 0.04363 | 0.89267 | 5.7 E-07 | 0.72356 | 0.01813 | 0.72356 | 0.00121 | 3.5 E-06 | 0,01746 | 16.85 | - | 5.09 |
10 | 3718336 | unknown | tttatttgttttcaggaaataaa | R | 0.88482 | 0.05522 | 0.88482 | 1.9 E-06 | - | - | - | - | 5.6 E-06 | - | - | - | - |
11 | 703043 | nagE nagB | tttaattcgtatcgcaaattaaa | L | 0.87827 | 0.05835 | 0.87827 | 1.6 E-06 | 0.65996 | 0.03449 | - | - | 9.0 E-06 | 0,06789 | - | - | 5.15 |
12 | 3913456 | glmU | gtttattcattgatcgaaataag | L | 0.87304 | 0.06097 | 0.87304 | 1.4 E-06 | 0.68260 | 0.03175 | 0.68260 | 0.00097 | 1.4 E-05 | 0,04487 | 16.45 | 1.0 | 5.01 |
13 | 707448 | chiP | tatttttcgcgacgcgaattatc | L | 0.86780 | 0.06372 | 0.86780 | 5.6 E-06 | - | - | - | - | 1.4 E-05 | - | - | - | - |
14 | 1292271 | tdk hns | atttattggcggcacaaaataaa | L | 0.86649 | 0.06450 | 0.86649 | 5.2 E-06 | - | - | - | - | 1.4 E-05 | - | - | - | - |
15 | 2531523 | ptsH | attattttgatgcgcgaaattaa | R | - | - | 0.86387 | 3.2 E-06 | - | - | - | - | 2.1 E-05 | - | - | - | - |
16 | 3217267 | aer patA | gttaattatcttgcccaaaaatc | R | - | - | 0.86518 | 3.6 E-06 | - | - | - | - | 2.1 E-05 | - | - | - | - |
17 | 4633489 | rob creA | gttatttaccgtgacgaactaat | R | - | - | 0.86518 | 4.2 E-06 | - | - | - | - | 2.1 E-05 | - | - | - | - |
18 | 1120757 | dinI | gttattttacctgtataaataac | L | - | - | 0.86126 | 8.2 E-06 | - | - | - | - | 2.1 E-05 | - | - | - | - |
19 | 2573887 | eutS | gttatttactctgacgaaaaatt | L | - | - | 0.86126 | 8.7 E-06 | - | - | - | - | 2.1 E-05 | - | - | - | - |
20 | 3086289 | galP | gttattttttattgtgaattaag | L | - | - | - | - | 0.69755 | 0.02567 | 0.69755 | 0.00155 | - | 0,02854 | - | - | - |
21 | 702949 | nagE nagB | cttattttatcattcaaaaaatc | L | - | - | - | - | 0.68969 | 0.02876 | 0.68969 | 0.00095 | - | 0,03596 | 16.06 | 1.0 | - |
22 | 1580729 | ydeN | gttgtttatcggcgagaaattac | L | - | - | - | - | 0.65082 | 0.03846 | - | - | - | 0,08240 | - | - | - |
23 | 1584727 | ydeP | cttattttttatattgaaaaata | L | - | - | - | - | - | - | - | - | - | - | 16.21 | 1.0 | 4.82 |
24 | 2628932 | unknown | gttttttatcttcaagaattata | L | - | - | - | - | - | - | - | - | - | - | 16.11 | - | - |
Time (s) | 12.58 ± 1.13 | 10.58 ± 0.27 | 6.61 ± 0.34 | 6.14 ± 0.47 | 749.25 ± 12.22 | 5.10 ± 0.38 | 23.3 ± 1.21 | 4.6 ± 0.09 | |||||||||