Table 8 Number of exon pairs (introns) tested per program, and the number of positive verifications
From: EGASP: the human ENCODE Genome Annotation Assessment Project
| Â | 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 | Â | Â | Â | Â | Â |
   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 | Â | Â | Â | Â | Â |
   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 | Â | Â | Â | Â | Â |
   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 | Â | Â | Â | Â | Â |
   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% |