Table 9 |
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|
Pfold predictions on both the high and medium similarity data-sets underflow on E. coli LSU rRNA. RNAalifold and Carnac, however, produce reasonable results. |
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|
E. coli LSU rRNA: Comparative Methods |
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|
|
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|
Algorithm |
number of bps in reference |
number of bps in prediction |
True Positives (% sensitivity) |
False Positives (% selectivity) |
Correlation (%) |
|
Plan A: ClustalW Alignment |
|||||
|
RNAalifold (H) |
794 |
879 |
627 (79.0) |
195 (76.3) |
0.776 (77.6) |
|
RNAalifold (H) + RNAfold-C |
794 |
871 |
629 (79.2) |
185 (77.3) |
0.782 (78.2) |
|
RNAalifold (M) |
819 |
721 |
614 (75.0) |
53 (92.1) |
0.831 (83.5) |
|
RNAalifold (M) + RNAfold-C |
819 |
790 |
691 (84.4) |
78 (89.9) |
0.871 (87.1) |
|
Pfold (H) |
794 |
0 |
0 (0.0) |
0 (0.0) |
0.000 (0.0) |
|
Pfold (M) |
819 |
0 |
0 (0.0) |
0 (0.0) |
0.000 (0.0) |
|
ILM (H) |
794 |
1048 |
389 (49.0) |
602 (39.3) |
0.438 (44.1) |
|
ILM (M) |
819 |
1161 |
560 (68.4) |
405 (58.0) |
0.630 (63.2) |
|
ILM-pknot (H) |
869 |
1048 |
272 (31.3) |
759 (26.4) |
0.287 (28.8) |
|
ILM-pknot (M) |
869 |
1161 |
377 (43.4) |
629 (37.5) |
0.403 (40.4) |
|
Plan B: Unaligned sequences |
|||||
|
Carnac (H) |
816 |
422 |
390 (47.8) |
7 (98.2) |
0.685 (73.0) |
|
Carnac (H) + RNAfold-C |
816 |
873 |
674 (82.6) |
156 (81.2) |
0.819 (81.9) |
|
Carnac (M) |
821 |
508 |
463 (56.4) |
14 (97.1) |
0.740 (76.7) |
|
Carnac (M) + RNAfold-C |
821 |
865 |
682 (83.1) |
147 (82.3) |
0.827 (82.7) |
|
|
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|
Gardner and Giegerich BMC Bioinformatics 2004 5:140 doi:10.1186/1471-2105-5-140 |
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