Table 1.
Coverage Results for the Different Programs on Human Sequence Alignments With Cat, Chicken, Cow, Dog, Pig, and Rat
| Coverage (bp) | Refseq | UTR | Time (sec) | |
| Cat | ||||
| AVID | 1200310 | 21966 | 13742 | 78 |
| BLASTZ | 1270696 | 22383 | 13632 | 101 |
| BLASTZ (chaining) | 1170350 | 21993 | 13632 | 52 |
| CHAOS | 360436 | 19022 | 7604 | 128 |
| GLASS | 1179833 | 21942 | 13426 | 9215 |
| MUMmer | 1092441 | 20604 | 12205 | 111 |
| Chicken | ||||
| AVID | 77114 | 17886 | 1742 | 35 |
| BLASTZ | 56370 | 19204 | 1357 | 11 |
| BLASTZ (chaining) | 56370 | 19204 | 1357 | 11 |
| CHAOS | 5635 | 3060 | 70 | 31 |
| GLASS | 56445 | 17437 | 984 | 2866 |
| MUMmer − | 18457 | 5634 | 0 | 24 |
| Chimp | ||||
| AVID | 852611 | 0 | 0 | 36 |
| BLASTZ | 881206 | 0 | 0 | 11330 |
| BLASTZ (chaining) | 854023 | 0 | 0 | 45 |
| CHAOS | −680491 | 0 | 0 | 4471 |
| GLASS | * | * | * | * |
| MUMmer − | 752809 | 0 | 0 | 5 |
| Cow | ||||
| AVID | 1195913 | 26359 | 10777 | 89 |
| BLASTZ | 1288895 | 27911 | 13505 | 79 |
| BLASTZ (chaining) | 1150323 | 25814 | 10434 | 57 |
| CHAOS | 317660 | 22551 | 6633 | 198 |
| GLASS | 1131693 | 25187 | 12860 | 10115 |
| MUMmer | 996019 | 22775 | 9621 | 135 |
| Dog | ||||
| AVID | 1015426 | 26278 | 11406 | 84 |
| BLASTZ | 1123496 | 27643 | 15321 | 91 |
| BLASTZ (chaining) | 973670 | 26131 | 11386 | 50 |
| CHAOS | 258696 | 22298 | 6182 | 173 |
| GLASS −− | 741066 | 20565 | 10364 | 7635 |
| MUMmer | 790831 | 22217 | 6848 | 116 |
| Pig | ||||
| AVID | 2163592 | 60903 | 22932 | 180 |
| BLASTZ | 2288008 | 65757 | 28016 | 168 |
| BLASTZ (chaining) | 2075031 | 61988 | 25900 | 110 |
| CHAOS | 574740 | 53854 | 9863 | 398 |
| GLASS − | 1951056 | 58207 | 23318 | 13689 |
| MUMmer | 1715068 | 55250 | 20505 | 235 |
| Rat | ||||
| AVID | 1686932 | 82920 | 38973 | 209 |
| BLASTZ | 2115917 | 90662 | 42267 | 447 |
| BLASTZ (chaining) | 1618195 | 83338 | 39099 | 101 |
| CHAOS | 456152 | 59918 | 14415 | 403 |
| GLASS −−−− − | 1076219 | 62978 | 29376 | 28993 |
| MUMmer | 850710 | 65361 | 31006 | 258 |
Coverage of the human genome using the mouse genome is described in O. . An asterisk indicates that the program was not able to successfully align the sequences. A minus sign indicates that the program crashed on one sequence pair. Multiple minus signs are used for multiple crashes. RefSeq annotations are based on the human December 2001 hg10 freeze.