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Table 1 Results on synthetic yeast-like data. Performance of various multiple sequence alignment programs on synthetic data generated with dinucleotide correlations that mimic actual yeast genomic data. q is the "proximity" of the species to their common ancestor, ie the probability that a given base is conserved from its common ancestor. This means that q2 is the conservation rate of bases in any pair of descendants. N+ is the number of bases correctly aligned. N- is the number of bases incorrectly aligned. Each data set consisted of 10 sets each containing N s sequences, each 1000 bases long, so the number of bases is 10000N S . Sen is the sensitivity, ie the ratio of number of bases correctly aligned to total number of bases, N+/(10000N s ). Er is the error rate, N-/(N+ + N-). sigma+ indicates sigma with a background model incorporating dinucleotide correlations. sigma— indicates sigma with an uncorrelated background model.

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 166 0 0.01 0.00 3210 0 0.11 0.00 28755 0 0.96 0.00
  sigma- 0 0 0.00 N/A 761 0 0.03 0.00 10737 0 0.36 0.00 29606 0 0.99 0.00
  dialign 0 0 0.00 N/A 266 0 0.03 0.00 854 0 0.04 0.00 9115 0 0.30 0.00
  alignm 320 136 0.01 0.30 6009 846 0.20 0.12 22710 1083 0.76 0.05 28258 434 0.94 0.02
  clustalw 15244 14756 0.51 0.49 25659 4341 0.86 0.14 28959 1041 0.97 0.03 29779 221 0.99 0.01
  mlagan 13691 16309 0.46 0.54 24766 5234 0.83 0.17 29596 404 0.99 0.01 30000 0 1.00 0.00
  tcoffee 3781 26219 0.13 0.87 15253 14747 0.51 0.49 26542 3458 0.88 0.12 29759 241 0.99 0.01
6 sigma+ 74 0 0.00 0.00 334 0 0.01 0.00 27765 24 0.46 0.00 57820 0 0.96 0.00
  sigma - 74 112 0.00 0.60 590 0 0.01 0.00 42882 40 0.71 0.00 58948 0 0.98 0.00
  dialign 66 158 0.00 0.71 604 176 0.01 0.23 7364 114 0.12 0.02 30871 0 0.51 0.00
  alignm 0 0 0.00 N/A 7192 123 0.12 0.02 53534 978 0.89 0.02 59326 222 0.99 0.00
  clustalw 29878 30122 0.50 0.50 52295 7705 0.87 0.13 57712 2288 0.96 0.04 59580 420 0.99 0.01
  mlagan 17411 42589 0.29 0.71 48105 11895 0.80 0.20 58736 1264 0.98 0.02 60000 0 1.00 0.00
  tcoffee 13215 46785 0.22 0.78 41965 18035 0.70 0.30 58084 1916 0.97 0.03 59925 75 1.00 0.00
9 sigma+ 0 0 0.00 N/A 597 0 0.01 0.00 41873 40 0.47 0.00 87769 0 0.98 0.00
  sigma - 160 64 0.00 0.29 2577 162 0.03 0.06 63579 228 0.71 0.00 88764 0 0.99 0.00
  dialign 78 264 0.00 0.77 1045 228 0.01 0.18 12162 176 0.14 0.01 54753 0 0.61 0.00
  alignm 44 159 0.00 0.78 29033 460 0.32 0.02 83545 960 0.93 0.01 89261 330 0.99 0.00
  clustalw 52761 37239 0.59 0.41 79733 10267 0.89 0.11 86758 3242 0.96 0.04 89429 571 0.99 0.01
  mlagan 16445 73555 0.18 0.82 68421 21579 0.76 0.24 88828 1172 0.99 0.01 90000 0 1.00 0.00
  tcoffee 27005 62995 0.30 0.70 67009 22991 0.74 0.26 88534 1466 0.98 0.02 89955 45 1.00 0.00