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Table 4 Results on uncorrelated data. Performance of various multiple sequence alignment programs on synthetic data with no dinucleotide correlations, and each base having probability 0.25. See the caption of Table 1 for explanation of the column and row labels.

From: Sigma: multiple alignment of weakly-conserved non-coding DNA sequence

   q = 0.35 q = 0.45 q = 0.55 q = 0.65
No embedded WM's
N s Prog N + N - Sen Er N + N - Sen Er N + N - Sen Er N + N - Sen Er
3 sigma- 0 0 0.00 N/A 260 0 0.01 0.00 11690 0 0.39 0.00 29154 0 0.97 0.00
  dialign 0 60 0.00 1.00 80 0 0.03 0.00 1000 0 0.06 0.00 7566 0 0.25 0.00
  alignm 0 0 0.00 N/A 6682 605 0.22 0.08 23338 656 0.78 0.03 28466 283 0.95 0.01
  clustalw 16675 13325 0.56 0.44 26450 3550 0.88 0.12 29340 660 0.98 0.02 29828 172 0.99 0.01
  mlagan 11280 18720 0.38 0.62 26874 3126 0.90 0.10 29767 233 0.99 0.01 30000 0 1.00 0.00
  tcoffee 3443 26557 0.11 0.89 12475 17525 0.42 0.58 27836 2164 0.93 0.07 29810 190 0.99 0.01
6 sigma- 0 0 0.00 N/A 0 0 0.00 N/A 23583 0 0.39 0.00 58986 0 0.98 0.00
  dialign 0 0 0.00 N/A 138 0 0.01 0.00 4588 0 0.08 0.00 28177 0 0.47 0.00
  alignm 0 0 0.00 N/A 13090 174 0.22 0.01 53252 824 0.89 0.02 59529 139 0.99 0.00
  clustalw 37040 22960 0.62 0.38 53438 6562 0.89 0.11 58432 1568 0.97 0.03 59727 273 1.00 0.00
  mlagan 15987 44013 0.27 0.73 50702 9298 0.85 0.15 58621 1379 0.98 0.02 59917 83 1.00 0.00
  tcoffee 13439 46561 0.22 0.78 35387 24613 0.59 0.41 58292 1708 0.97 0.03 59941 59 1.00 0.00