Table 2.
Cross species ranks —this table shows the results of aligning the cDNAs of mouse, rat and humans to the mouse genome
| Aligner | Mouse | Rank | Rat | Rank | Human | Rank |
|---|---|---|---|---|---|---|
| Blat | 97.23 | 6 | 71.29 | 18 | 43.79 | 17 |
| BlatX | 95.21 | 13 | 35.7 | 22 | 9.27 | 22 |
| Est2Genome | 94.38 | 15 | 85.14 | 10 | 75.67 | 9 |
| Est2Genome+ | 95.15 | 14 | 76.22 | 15 | 56.63 | 14 |
| Exalin | 97.3 | 5 | 87.77 | 7 | 78.11 | 7 |
| Exonerate | 95.5 | 12 | 85.17 | 9 | 63.57 | 10 |
| ExonerateCG | 96.42 | 10 | 84.26 | 12 | 59.05 | 13 |
| ExonerateDG | 96.16 | 11 | 84.36 | 11 | 59.78 | 12 |
| GeneSeqer | 74.81 | 21 | 64.28 | 19 | 50.33 | 16 |
| GMap | 93.13 | 16 | 82.39 | 13 | 60.74 | 11 |
| Pairagon | 98.88 | 1 | 91.59 | 2 | 77.04 | 8 |
| PairagonX | 98.79 | 2 | 92.15 | 1 | 87.24 | 1 |
| Palma | 96.52 | 9 | 77.8 | 14 | 33.28 | 20 |
| Sim4 | 91.94 | 19 | 76.03 | 16 | 35.48 | 18 |
| Sim4+ | 92.5 | 18 | 75.49 | 17 | 35.05 | 19 |
| Spaln | 97.51 | 3 | 90.11 | 4 | 82.68 | 5 |
| SpalnX | 96.89 | 8 | 90.09 | 5 | 86.67 | 2 |
| Spidey | 88.53 | 20 | 48.05 | 21 | 13.1 | 21 |
| SpideyX | 70.1 | 22 | 61.7 | 20 | 52.94 | 15 |
| Splign | 97.46 | 4 | 90.21 | 3 | 82.94 | 4 |
| SplignX | 97.19 | 7 | 89.88 | 6 | 86.1 | 3 |
| Xat | 92.78 | 17 | 85.59 | 8 | 79.19 | 6 |
For each aligner, we show the product of exon specificity and sensitivity (as in Fig. 3) and the rank of the aligner, which shows which aligners were the most accurate.