Table 3.
Comparison of performance with human chromosome 20 - mouse chromosome 2 pair.
| length (bp) | Sn (%) | Spmam (%) | time | memory (GB) | |
|---|---|---|---|---|---|
| Blastz (default) | 18,598,895 | 85.9 | 57.5 | 66 m 40 s | 1.6 |
| Blastz (T = 2 C = 2) | 16,353,601 | 85.1 | 95.5 | 9 m 45 s | 1.6 |
| Blastz* (T = 2 C = 2) | 16,665,937 | 85.3 | 80.8 | 12 m 20 s | 0.4 |
| NUCmer | 1,118,494 | 5.8 | 75.2 | 3 m 55 s | 1.0 |
| Cgaln (-X2500 k = 11) | 13,964,626 | 79.2 | 92.3 | 2 m 14 s | 0.8 |
| Cgaln (-X2500 k = 12) | 15,154,530 | 81.4 | 90.6 | 2 m 16 s | 1.1 |
Performance of alignment programs examined on human chromosome 20 (chr20) vs. mouse chromosome 2 (chr2). The row of Blastz with the symbol "*" refers to the examination on split chromosomal sequences. The threshold Tcol was set to "-X2500". Spmam is evaluated as the ratio of the coverage with human chr20 - mouse chr2 to that with the human chr20 - whole-genome sequence of mouse.