Table 2.
Test scenario 1: Reconstruction of the Loxodonta africana dynein heavy chain genes in the whole genome sequence based on human protein sequences
| Tool | Predicted genes | Missing exons1 | Wrong exons2 | Exon sens. % | Exon sens. (ov.)3 % | Exon spec. % | Nucl. sens. % | Nucl. spec. % | Execution time per prot. seq. |
|---|---|---|---|---|---|---|---|---|---|
| Scipio 1.54 | 16 | 11 | 6 | 93.4 | 99.1 | 93.3 | 98.7 | 99.8 | 70 m 46s |
| Exonerate5 | 2145 | 6 | 5669 | 94.8 | 99.5 | 16.5 | 99.7 | 18.5 | 123 m 23s |
| Exonerate6 | 16 | 287 | 62 | 73.4 | 76.1 | 90.2 | 76.1 | 94.3 | 121 m 27s |
| Augustus7 | 1374928 | 0 | 3909434 | 47.9 | 100.0 | 0.0 | 100.0 | 0.3 | > 10 days |
| BLAT8 | - | 9 | 264228 | 19.6 | 99.3 | 0.1 | 97.4 | 2.6 | 7 m 24s |
| Scipio 1.04 | 16 | 14 | 46 | 86.1 | 98.8 | 83.2 | 97.9 | 99.4 | 8 m 24s |
1 Number of annotated exons, which are not overlapped by any predicted exon
2 Number of predicted exons, which are not overlapped by any annotated exon
3 Number annotated exons, which are overlapped by at least one predicted exon divided by the number of annotated exons
4 Mammalia cross species default options (for detailed parameters see Additional file 5)
5 Parameters: --model protein2genome
6 Parameters: --model protein2genome --bestn 1
7 Parameters: --species = human --genemodel = exactlyone (for more parameters see Additional file 5)
8 Parameters as in 4: -tileSize = 7 -minIdentity = 54 -minScore = 15 -oneOff = 1