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Table 2 Averaged ranks derived from Friedman rank sum tests for ClustalW's gap parameter optimization.

From: An enhanced RNA alignment benchmark for sequence alignment programs

  ge
go 0.42 0.83 1.67 3.33 4.99 6.66 8.32 9.99
7.5 56.0 55.0 54.0 53.0 51.2 50.0 47.0 42.8
11.25 47.5 44.0 41.5 37.2 34.5 27.3 28.2 31.5
15.0 20.8 24.0 20.0 14.5 13.5 15.5 22.3 29.3
18.75 10.8 8.3 8.2 7.5 11.3 20.8 27.5 35.8
22.5 4.7 2.8 3.7 8.8 17.7 27.0 34.5 39.2
26.25 5.8 5.5 8.8 17.5 31.2 36.7 42.3 46.2
30.0 15.2 17.2 22.8 32.8 39.3 45.0 49.0 51.5
  1. Ranks (smaller values mean better performance) for each gap-open (go)/gap-extension (ge) penalty combination are based on the BRALISCORE averaged over all alignment sets with k {2, 3, 5, 7, 10, 15} sequences and APSI ≤ 80 %. CLUSTALW's default and the optimized value combinations are given in bold-face.