ASPic-GeneID: A Lightweight Pipeline for Gene Prediction and Alternative Isoforms Detection
Table 1
Accuracy of gene finding programs on the complete C. elegans genome.
Evaluation at gene level
Program
SNg
SPg
SSg
WG
MG
SNe
SPe
SSe
WE
ME
SNi
SPi
SSi
WI
MI
SNn
SPn
SSn
GeneID
0.97
0.83
0.90
0.19
0.03
0.67
0.69
0.68
0.16
0.15
0.70
0.74
0.72
0.26
0.30
0.87
0.88
0.87
ASPic
0.34
0.96
0.65
0.03
0.66
0.29
0.91
0.60
0.02
0.69
0.30
0.97
0.63
0.03
0.70
0.31
0.98
0.64
ASPic-GeneID
0.99
0.93
0.96
0.09
0.01
0.85
0.81
0.83
0.08
0.03
0.93
0.88
0.90
0.12
0.07
0.95
0.95
0.95
ASPic-GeneID_AS1
0.99
0.75
0.87
0.21
0.01
0.87
0.78
0.82
0.12
0.02
0.93
0.86
0.89
0.14
0.07
0.96
0.91
0.93
ASPic-GeneID_AS2
0.98
0.98
0.98
0.07
0.02
0.86
0.83
0.84
0.07
0.03
0.94
0.89
0.91
0.11
0.06
0.96
0.93
0.94
TWINSCAN
0.95
0.87
0.91
0.12
0.05
0.76
0.77
0.76
0.11
0.11
0.81
0.83
0.82
0.17
0.19
0.90
0.91
0.90
TWINSCAN_EST
0.95
0.88
0.91
0.09
0.05
0.79
0.81
0.80
0.09
0.09
0.84
0.87
0.85
0.13
0.16
0.91
0.92
0.91
FGENESH
0.97
0.88
0.92
0.10
0.03
0.76
0.74
0.75
0.13
0.09
0.80
0.79
0.79
0.21
0.20
0.93
0.89
0.91
Genefinder
0.95
0.97
0.96
0.05
0.05
0.77
0.74
0.75
0.13
0.08
0.83
0.78
0.80
0.22
0.17
0.93
0.89
0.91
SNAP
0.96
0.69
0.82
0.22
0.04
0.70
0.66
0.68
0.18
0.12
0.74
0.73
0.73
0.27
0.26
0.90
0.86
0.88
Evaluation at transcript level
Program
SNt
SPt
SSt
WT
MT
SNet
SPet
SSet
WEt
MEt
SNit
SPit
SSit
WIt
TMIt
SNnt
SPnt
SSnt
GeneID
0.23
0.23
0.23
0.05
0.19
0.68
0.70
0.69
0.17
0.18
0.70
0.72
0.71
0.28
0.30
0.84
0.87
0.85
ASPic
0.26
0.71
0.48
0.01
0.29
0.81
0.95
0.88
0.01
0.15
0.82
0.98
0.90
0.02
0.18
0.81
0.99
0.90
ASPic-GeneID
0.44
0.47
0.45
0.03
0.17
0.86
0.81
0.83
0.10
0.05
0.92
0.85
0.88
0.15
0.08
0.93
0.93
0.93
ASPic-GeneID_AS1
0.53
0.44
0.48
0.08
0.11
0.87
0.85
0.86
0.08
0.06
0.91
0.88
0.89
0.12
0.09
0.92
0.94
0.93
ASPic-GeneID_AS2
0.46
0.50
0.48
0.03
0.17
0.88
0.81
0.84
0.11
0.04
0.94
0.85
0.89
0.15
0.06
0.95
0.90
0.92
TWINSCAN
0.35
0.36
0.35
0.04
0.15
0.77
0.78
0.77
0.11
0.12
0.81
0.82
0.81
0.18
0.19
0.88
0.91
0.89
TWINSCAN_EST
0.43
0.45
0.44
0.04
0.13
0.80
0.83
0.81
0.08
0.11
0.84
0.87
0.85
0.13
0.16
0.89
0.93
0.91
FGENESH
0.32
0.33
0.32
0.06
0.16
0.75
0.76
0.75
0.13
0.13
0.78
0.79
0.78
0.21
0.22
0.88
0.89
0.88
Genefinder
0.30
0.35
0.32
0.05
0.18
0.79
0.73
0.76
0.16
0.10
0.83
0.75
0.79
0.25
0.17
0.91
0.86
0.88
SNAP
0.27
0.22
0.24
0.09
0.11
0.67
0.73
0.70
0.11
0.19
0.70
0.77
0.73
0.23
0.30
0.82
0.92
0.87
The highest values are shown in bold. SN indicates sensitivity. SP indicates specificity. SS indicates the average between SN and SP. Gene (g), transcript (t), exon (e), intron (i), and nucleotide (n) were assessed.
