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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.

From: CONTRAST: a discriminative, phylogeny-free approach to multiple informant de novogene prediction

  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