Table 2.
FGENESH gene predictions and comparisons to homology-based inferences.
| FGENESH Model | Predicted genes | Unsupported predictions1 | Gene mergers2 | Genes merged2 | Validated starts3 | Validated stops3 | Validated starts + stops |
|---|---|---|---|---|---|---|---|
| At | 159 | 32 | 5 | 10 | 80 | 68 | 148 |
| Mt | 163 | 34 | 4 | 8 | 80 | 72 | 152 |
| Mo | 115 | 9 | 12 | 27 | 66 | 64 | 130 |
| Nt | 208 | 65 | 3 | 7 | 70 | 63 | 133 |
| Le | 149 | 33 | 8 | 17 | 69 | 65 | 134 |
| Vv | 121 | 14 | 16 | 38 | 65 | 62 | 127 |
1FGENESH predictions were classified as unsupported if no gene was detected at the indicated location via Blast homology searches.
2The term "gene merger" refers to instances in which two or more gene sites identified on the basis of Blast homology were merged into a single FGENESH gene prediction. The term "genes merged" refers to the cumulative number of genes involved in such gene mergers.
3FGENESH predictions of start and stop codons were considered to be validated if support for their predicted locations was obtained from examination of ORFs in homologous sequences identified by Blast homology searches.