Table 3

Generally the comparative approaches perform much better than MFE methods at determining S. cerevisiae tRNA-PHE structure. For the consensus predictions of RNAalifold and Carnac we also computed "filled" structures using constrained MFE predictions. This usually improved the sensitivity of the methods. PFold a built-in stem-extension procedure to fill structures. As the tRNA structure contains a multi-loop Foldalign is not expected to perform well here. Dynalign performed well on the most diverse data-set (M) but didn't do well on the high similarity data-set. The structure alignment methods generally did poorly here. Most probably due to the miss-folded MFE structure which were used as input. Trimming high entropy base-pairs from the input structures produced modest improvements.

S. cerevisiae tRNA-PHE: Comparative Methods


Algorithm

number of bps in reference

number of bps in prediction

True Positives (% sensitivity)

False Positives (% selectivity)

Correlation (%)


Plan A: ClustalW Alignment

RNAalifold (H)

21

20

19 (90.5)

0 (100.0)

0.950 (95.2)

RNAalifold (H) + RNAfold-C

21

21

21 (100.0)

0 (100.0)

1.000 (100.0)

RNAalifold (M)

18

14

14 (77.8)

0 (100.0)

0.880 (88.9)

RNAalifold (M) + RNAfold-C

18

21

18 (100.0)

0 (100.0)

1.000 (100.0)

ILM (H)

21

24

16 (76.2)

7 (69.6)

0.722 (72.9)

ILM (M)

18

30

18 (100.0)

6 (75.0)

0.863 (87.5)

Pfold (H)

21

21

20 (95.2)

0 (100.0)

0.975 (97.6)

Pfold (M)

18

21

18 (100.0)

0 (100.0)

1.000 (100.0)

Plan B: Unaligned sequences

Carnac (H)

21

17

15 (71.4)

1 (93.8)

0.815 (82.6)

Carnac (H) + RNAfold-C

21

21

19 (90.5)

1 (95.0)

0.925 (92.7)

Carnac (M)

21

13

12 (57.1)

1 (92.3)

0.722 (74.7)

Carnac (M) + RNAfold-C

21

22

16 (76.2)

5 (76.2)

0.757 (76.2)

Dynalign (H)

21

22.40

11.50 (54.78)

10.20 (54.45)

0.5353 (54.59)

Dynalign (M)

21

21.10

19.80 (94.27)

1.20 (95.00)

0.9448 (94.64)

Foldalign (H)

21

16

5 (23.8)

11 (31.2)

0.259 (27.5)

Foldalign (M)

21

16

5 (23.8)

10 (33.3)

0.268 (28.6)

Plan C: Structure alignment

MARNA (H)

21

19

6 (28.6)

12 (33.3)

0.295 (31.0)

MARNA (M)

21

22

7 (33.3)

15 (31.8)

0.311 (32.6)

MARNA-trim (H)

21

6

6 (28.6)

0 (100.0)

0.530 (64.3)

MARNA-trim (M)

21

15

15 (71.4)

0 (100.0)

0.843 (85.7)

RNAforester (H)

21

23

6 (28.6)

16 (27.3)

0.263 (27.9)

RNAforester (M)

21

21

14 (66.7)

7 (66.7)

0.659 (66.7)


Gardner and Giegerich BMC Bioinformatics 2004 5:140   doi:10.1186/1471-2105-5-140

Open Data