Table 7.
Characteristics of Gene Prediction Accuracy for the E. coliGenome with 4289 Annotated Genes
| Models | AT cluster type | Sn | Sp | Average (Sn, Sp) | No. of correctly predicted genes | No. of predictions |
| GB | 0.908 | 0.978 | 0.943 | 3895 | 3981 | |
| R | 0.851 | 0.988 | 0.919 | 3651 | 3696 | |
| AT | 2A | 0.925 (0.923) | 0.982 (0.983) | 0.954 | 3968 | 4039 |
| AT,T | 2A | 0.931 (0.929) | 0.981 (0.982) | 0.956 | 3995 | 4073 |
| R,AT,T | 2A | 0.932 | 0.978 | 0.955 | 3999 | 4087 |
| T | 2A | 0.835 (0.834) | 0.991 (0.991) | 0.913 | 3580 | 3614 |
| AT | 2B | 0.916 (0.911) | 0.985 (0.985) | 0.951 | 3930 | 3991 |
| AT,T | 2B | 0.922 (0.917) | 0.983 (0.983) | 0.953 | 3954 | 4023 |
| R,AT,T | 2B | 0.922 | 0.983 | 0.953 | 3954 | 4023 |
| T | 2B | 0.859 (0.857) | 0.990 (0.990) | 0.924 | 3683 | 3719 |
| AT | 2C | 0.924 (0.924) | 0.980 (0.981) | 0.952 | 3964 | 4043 |
| AT,T | 2C | 0.939 (0.938) | 0.979 (0.979) | 0.959 | 4027 | 4113 |
| R,AT,T | 2C | 0.939 | 0.979 | 0.959 | 4027 | 4113 |
| T | 2C | 0.848 (0.845) | 0.990 (0.990) | 0.919 | 3639 | 3674 |
| AT | 3A | 0.927 (0.924) | 0.982 (0.983) | 0.955 | 3975 | 4048 |
| AT,HT,T | 3A | 0.936 | 0.978 | 0.957 | 4014 | 4103 |
| AT,T | 3A | 0.934 (0.930) | 0.980 (0.981) | 0.957 | 4004 | 4085 |
| HT | 3A | 0.716 (0.715) | 0.989 (0.991) | 0.853 | 3070 | 3103 |
| R,AT,T | 3A | 0.934 | 0.980 | 0.957 | 4004 | 4085 |
| R,AT,T,HT | 3A | 0.936 | 0.978 | 0.957 | 4014 | 4103 |
| T | 3A | 0.852 (0.850) | 0.990 (0.990) | 0.921 | 3653 | 3689 |
| AT | 3B | 0.922 (0.916) | 0.984 (0.984) | 0.953 | 3956 | 4022 |
| AT,HT,T | 3B | 0.931 | 0.980 | 0.956 | 3993 | 4076 |
| AT,T | 3B | 0.929 (0.922) | 0.982 (0.982) | 0.956 | 3983 | 4058 |
| HT | 3B | 0.713 (0.715) | 0.990 (0.991) | 0.851 | 3057 | 3089 |
| R,AT,T | 3B | 0.929 | 0.982 | 0.956 | 3983 | 4058 |
| R,AT,T,HT | 3B | 0.931 | 0.980 | 0.956 | 3993 | 4076 |
| T | 3B | 0.872 (0.869) | 0.989 (0.989) | 0.930 | 3741 | 3781 |
| AT | 3C | 0.926 (0.922) | 0.980 (0.980) | 0.953 | 3971 | 4052 |
| AT,HT,T | 3C | 0.943 | 0.976 | 0.960 | 4046 | 4146 |
| AT,T | 3C | 0.941 (0.938) | 0.977 (0.978) | 0.959 | 4035 | 4128 |
| HT | 3C | 0.713 (0.717) | 0.990 (0.992) | 0.851 | 3057 | 3089 |
| R,AT,T | 3C | 0.941 | 0.977 | 0.959 | 4035 | 4128 |
| R,AT,T,HT | 3C | 0.943 | 0.976 | 0.960 | 4046 | 4146 |
| T | 3C | 0.863 (0.860) | 0.989 (0.990) | 0.926 | 3701 | 3741 |
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The results obtained by using preclustering cross validation are shown in parentheses (italics). Boldface numbers show the maximum postclustering value of Avg(Sn, Sp) for a given species.
