Table 3 Segregation success and run-times (in parentheses) for different combinations of peptide lengths (used to calculate sequence similarity) and the degree of ‘softening’ used to reduce the amino acid alphabet
From: Reduction, alignment and visualisation of large diverse sequence families
Soft | Peptide length | Â | |||
|---|---|---|---|---|---|
| Â | 3 | 4 | 5 | 6 | 7 |
0 | 21 (10.26) | 21 (10.64) | 20 (10.96) | 20 (11.12) | 20 (10.81) |
| Â | 23 (124.5) | 22 (125.0) | 21 (121.1) | 20 (115.5) | 31 (111.2) |
1 | 25 (10.33) | 24 (10.70) | 20 (10.96) | 24 (11.15) | 24 (11.04) |
| Â | 34 (127.7) | 26 (125.7) | 33 (124.1) | 35 (117.6) | 79 (125.1) |
2 | 24 (10.45) | 22 (10.90) | 24 (11.12) | 24 (11.28) | 28 (11.16) |
| Â | 43 (128.7) | 36 (128.0) | 43 (126.1) | 50 (121.2) | 71 (130.0) |
3 | 33 (10.44) | 29 (10.84) | 29 (11.23) | 30 (11.60) | 28 (11.35) |
| Â | 60 (129.8) | 58 (130.9) | 69 (127.4) | 59 (122.5) | 75 (132.0) |
4 | 31 (10.31) | 31 (10.92) | 32 (11.12) | 35 (11.62) | 36 (11.42) |
| Â | 69 (132.3) | 75 (132.0) | 71 (130.0) | 79 (125.1) | 69 (132.3) |