Table 2.

Performance of Ab Initio Programs on HMR195 Data Set on Adding Similarity Information

Nucleotide level
Exon level
Program
No. genes
SEN
SPE
AC
CC
CR
PC
OL
ME
WE
ESEN
ESPE
EAVG
GENSCAN 3 0.93 0.89 0.91 0.89 735 131 10 76 104 0.70 0.69 0.70
GENSCAN+BLASTX 0 0.98 0.89 0.92 0.92 799 110 11 36 176 0.81 0.73 0.77
GENSCAN+BLASTX+BLASTN 0 0.97 0.90 0.92 0.92 801 101 9 45 163 0.81 0.74 0.78
HMMgene 5 0.90 0.90 0.91 0.89 715 98 11 128 81 0.74 0.75 0.75
HMMgene+BLASTX 0 0.95 0.93 0.93 0.93 779 91 15 68 91 0.80 0.78 0.79
HMMgene+BLASTX+BLASTN 0 0.95 0.95 0.94 0.93 780 86 13 74 74 0.80 0.80 0.80
EUI 3 0.92 0.94 0.93 0.91 769 74 4 104 55 0.77 0.81 0.79
EUI+BLASTX 0 0.96 0.94 0.94 0.94 795 86 8 63 65 0.80 0.81 0.81
EUI+BLASTX+BLASTN 0 0.95 0.96 0.95 0.94 795 81 7 69 53 0.80 0.83 0.82
EUI-FRAME 3 0.92 0.94 0.93 0.91 762 70 5 115 46 0.77 0.82 0.79
EUI-FRAME+BLASTX 0 0.96 0.95 0.94 0.94 793 84 9 67 56 0.80 0.82 0.81
EUI-FRAME+BLASTX+BLASTN 0 0.95 0.96 0.95 0.94 793 79 8 73 48 0.80 0.83 0.82
GI 15 0.84 0.89 0.90 0.84 742 57 3 149 43 0.72 0.80 0.76
GI+BLASTX 0 0.95 0.95 0.94 0.94 796 78 7 71 56 0.80 0.83 0.82
GI+BLASTX+BLASTN 0 0.94 0.97 0.94 0.94 796 70 6 77 45 0.80 0.85 0.83
GENOMESCAN
1
0.96
0.87
0.91
0.90
781
115
16
45
213
0.78
0.71
0.74