Table 8

Number of exon pairs (introns) tested per program, and the number of positive verifications

Number of tested exon pairs

Number of positive RT-PCR exon pairs and % over tested

Number of tested exon pairs suported by TARs/transfrags and % over tested pairs

Number of positive RT-PCR pairs supported by TARs/transfrags and % over supported pairs

% of positive RT-PCR pairs supported by TARs/transfrags over positive

Category 1

AUGUSTUS-any

31

2 (6.5%)

3 (9.7%)

1 (33.3%)

50.0%

FGENESH++

119

3 (2.5%)

3 (2.5%)

1 (33.3%)

33.3%

JIGSAW

19

2 (10.5%)

3 (15.8%)

1 (33.3%)

50.0%

PAIRAGON-any

1

0 (0.0%)

0 (0.0%)

0 (0.0%)

0.0%

Category 2

AUGUSTUS-abinit

29

2 (6.9%)

2 (6.9%)

1 (50.0%)

50.0%

GENEMARK.hmm

99

1 (1.0%)

3 (3.0%)

1 (33.3%)

100.0%

GENEZILLA

34

2 (5.9%)

1 (2.9%)

0 (0.0%)

0.0%

Category 3

ACEVIEW

13

4 (30.8%)

2 (15.4%)

2 (100.0%)

50.0%

AUGUSTUS-EST

31

2 (6.5%)

3 (9.7%)

1 (33.3%)

50.0%

ENSEMBL

10

1 (10.0%)

2 (20.0%)

1 (50.0%)

100.0%

EXOGEAN

18

1 (5.6%)

3 (16.7%)

1 (33.3%)

100.0%

EXONHUNTER

23

1 (4.3%)

2 (8.7%)

0 (0.0%)

0.0%

PAIRAGON+NSCAN_EST

1

0 (0.0%)

0 (0.0%)

0 (0.0%)

0.0%

Category 4

AUGUSTUS-dual

26

1 (3.8%)

3 (11.5%)

1 (33.3%)

100.0%

DOGFISH

11

2 (18.2%)

1 (9.1%)

1 (100.0%)

50.0%

MARS

47

7 (14.9%)

5 (10.6%)

3 (60.0%)

42.9%

NSCAN

26

0 (0.0%)

2 (7.7%)

0 (0.0%)

0.0%

SAGA

9

0 (0.0%)

1 (11.1%)

0 (0.0%)

0.0%

All unique exon pairs

238

7 (2.9%)

7 (2.9%)

3 (42.9%)

42.9%

The percentage of success has been computed in the table on the 238 selected exon pairs. For technical reasons, only 221 of them could be tested by RT-PCR. In the text the percentages are given with respect to this number.

Guigó et al. Genome Biology 2006 7(Suppl 1):S2   doi:10.1186/gb-2006-7-s1-s2