Table 7

Exons predicted by the programs not overlapping GENCODE annotated exons, and supported by transfrag evidence from genome tiling microarrays

Total number of unique exons

Number of exons overlapping TARs/transfrags (%)

Number of non-annotated exons

Number of non-annotated exons overlapping TARs/transfrags (%)

Number of intergenic exons

Number of Intergenic exons overlapping TARs/transfrags (%)

Category 1

AUGUSTUS-any

4,160

2,718 (65.3%)

484

74 (15.3%)

281

38 (13.5%)

FGENESH++

4,784

2,766 (57.8%)

1,071

146 (13.6%)

885

123 (13.9%)

JIGSAW

3,935

2,673 (67.9%)

206

34 (16.5%)

130

19 (14.6%)

PAIRAGON-any

4,414

3,080 (69.8%)

284

84 (29.6%)

221

68 (30.8%)

Category 2

AUGUSTUS-abinit

3,699

2,336 (63.2%)

776

175 (22.6%)

482

111 (23.0%)

GENEMARK.hmm

6,897

2,552 (37.0%)

3,796

319 (8.4%)

2,826

244 (8.6%)

GENEZILLA

3,415

1,535 (44.9%)

1,361

110 (8.1%)

970

69 (7.1%)

Category 3

ACEVIEW

8,410

5,756 (68.4%)

539

118 (21.9%)

449

106 (23.6%)

AUGUSTUS-EST

4,073

2,700 (66.3%)

439

73 (16.6%)

253

37 (14.6%)

ENSEMBL

4,505

3,094 (68.7%)

251

27 (10.8%)

187

17 (9.1%)

EXOGEAN

5,014

3,480 (69.4%)

183

21 (11.5%)

100

15 (15.0%)

EXONHUNTER

6,376

2,843 (44.6%)

2,782

257 (9.2%)

2,055

187 (9.1%)

PAIRAGON+NSCAN_EST 4,404

3,073 (69.8%)

284

84 (29.6%)

221

68 (30.8%)

Category 4

AUGUSTUS-dual

4,024

2,588 (64.3%)

629

114 (18.1%)

364

65 (17.9%)

DOGFISH

3,194

2,290 (71.7%)

267

115 (43.1%)

225

99 (44.0%)

MARS

4,623

2,801 (60.6%)

948

161 (17.0%)

528

89 (16.9%)

NSCAN

3,996

2,686 (67.2%)

500

133 (26.6%)

342

92 (26.9%)

SAGA

2,115

1,147 (54.2%)

564

36 (6.4%)

433

26 (6.0%)

All unique exons (18 progs)

26,818

12,001 (44.7%)

12,025

1,563 (13.0%)

8,634

1,163 (13.5%)

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