Table 4

Performance on the EGASP test regions. Sensitivity (Sn) and specificity (Sp) are shown at the nucleotide (Nuc), exon, transcript (Trans) and gene levels for CONTRAST and the 19 predictors entered in the EGASP experiment. At each level of evaluation, the performance of the predictor with the highest average sensitivity and specificity for a given category is shown in bold. Also shown is the performance of the UCSC RefGene track, which consists of RefSeq cDNAs aligned to the genome. The track was evaluated just before the start of the EGASP workshop.

Nuc Sn
 Nuc Sp
 Exon Sn
 Exon Sp
 Trans Sn
 Trans Sp
 Gene Sn
 Gene Sp
RefGene Track
 85.34
 98.50
 73.23
 94.67
 41.91
 75.21
 77.03
 82.56









Category 1 (any information)
AUGUSTUS-any
 94.42
 82.43
 74.67
 76.76
 22.65
 35.59
 47.97
 35.59
FGENESH++
 91.09
 76.89
 75.18
 69.31
 36.21
 41.61
 69.93
 42.09
JIGSAW
 94.56
 92.19
 80.61
 89.33
 34.05
 65.95
 72.64
 65.95
PAIRAGON-any
 87.77
 92.78
 76.85
 88.91
 39.29
 60.34
 69.59
 61.32









Category 2 (target sequence)
AUGUSTUS-abinit
 78.65
 75.29
 52.39
 62.93
 11.09
 17.22
 24.32
 17.22
GENEMARK.hmm-A
 78.43
 37.97
 50.58
 29.01
 6.93
 3.24
 15.20
 3.24
GENEMARK.hmm-B
 76.09
 62.94
 48.15
 47.25
 7.70
 7.91
 16.89
 7.91
GENEZILLA
 87.56
 50.93
 62.08
 50.25
 9.09
 8.84
 19.59
 8.84









Category 3 (protein, mRNA, EST)
ACEVIEW
 90.94
 79.14
 85.75
 56.98
 44.68
 19.31
 63.51
 48.65
AUGUSTUS-EST
 92.62
 83.45
 74.10
 77.40
 22.50
 37.01
 47.64
 37.01
ENSEMBL
 90.18
 92.02
 77.53
 82.65
 39.75
 54.64
 71.62
 67.32
EXOGEAN
 84.18
 94.33
 79.34
 83.45
 42.53
 52.44
 63.18
 80.82
EXONHUNTER
 90.46
 59.67
 64.44
 41.77
 10.48
 6.33
 21.96
 6.33
PAIRAGON+NSCAN_EST
 87.56
 92.77
 76.63
 88.95
 39.29
 60.64
 69.59
 61.71









Category 4 (genomic alignments)
CONTRAST
 94.44
 89.25
 77.68
 86.02
 25.12
 47.87
 53.04
 47.87
AUGUSTUS-dual
 88.86
 80.15
 63.06
 69.14
 12.33
 18.64
 26.01
 18.64
DOGFISH
 64.81
 88.24
 53.11
 77.34
 5.08
 14.61
 10.81
 14.61
MARS
 84.25
 74.13
 65.56
 61.65
 15.87
 15.11
 33.45
 24.94
NSCAN
 85.38
 89.02
 67.66
 82.05
 16.95
 36.71
 35.47
 36.71
SAGA
 52.54
 81.39
 38.82
 50.73
 2.16
 3.44
 4.39
 3.44

Gross et al. Genome Biology 2007 8:R269   doi:10.1186/gb-2007-8-12-r269

Open Data