Table 1 Segregation success and run-times for different clustering strategies are tabulated for: a) a single peptide pre-sort with increasing numbers of alignment cycles, b) staged alignment cycles from 90 to 50 % identity each with a peptide presort (using 1 pass), c) as for (b) but with multiple pre-sort cycles indicated in parentheses)
From: Reduction, alignment and visualisation of large diverse sequence families
a | Single pre-sort | ||
|---|---|---|---|
Alignment | Time | Sequences | Remaining |
stages (to 50 %) | sec. | selected | subfamilies |
1 | 58.8 | 1658 | 503 |
2 | 91.4 | 355 | 302 |
3 | 226.1 | 196 | 171 |
4 | 462.6 | 175 | 154 |
5 | 727.1 | 172 | 151 |
b | Staged pre-sort | ||
Alignment | Time | Sequences | Remaining |
stages (3 to X%) | sec. | selected | subfamilies |
90 (1) | 36.30 | 1597 | 947 |
80 (1) | 1.33 | 563 | 314 |
70 (1) | 1.00 | 165 | 31 |
60 (1) | 0.53 | 104 | 24 |
50 (1) | 0.47 | 71 | 21 |
c | Staged (multi-pass) pre-sort | ||
Alignment | Time | Sequences | Remaining |
stages (3 to X%) | sec. | selected | subfamilies |
90 (8) | 10.62 | 3641 | 598 |
80 (4) | 4.26 | 1034 | 93 |
70 (2) | 2.31 | 285 | 40 |
60 (1) | 1.10 | 98 | 20 |
50 (1) | 0.42 | 62 | 21 |