Skip to main content

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  
  3 4 5 6 7
0 21 (10.26) 21 (10.64) 20 (10.96) 20 (11.12) 20 (10.81)
  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)
  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)
  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)
  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)
  69 (132.3) 75 (132.0) 71 (130.0) 79 (125.1) 69 (132.3)
  1. Two sets of values are reported for each combination corresponding to starting sets of 10 and 30K sequences. The values are the number of final families and the time in seconds taken for the first peptide based pre-sort