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Table 2 Yeast benchmark: effect of parameters

From: Sigma-2: Multiple sequence alignment of non-coding DNA via an evolutionary model

Program dataset Matches per basea dataset Matches per basea Difference
Sigma-2 (defaults) orthologous 1.9893 shuffled 0.0031 1.9862
Sigma-2 (no bg model) orthologous 2.1319 shuffled 0.0133 2.1186
Sigma-2(no tr mat) orthologous 1.9115 shuffled 0.0046 1.9069
Sigma-2(no bg, no tr) orthologous 2.3799 shuffled 0.0275 2.3524
Sigma-2(p 0.2) orthologous 2.4139 shuffled 0.0389 2.3750
Sigma-2(p 0.2, no bg, no tr) orthologous 2.5615 shuffled 0.0586 2.5029
FSA (defaults) orthologous 2.7996 shuffled 0.3572 2.4424
FSA (gap5) orthologous 2.4695 shuffled 0.1465 2.3230
Dialign-TX (defaults) orthologous 2.9501 shuffled 0.8576 2.0925
Dialign-TX (-l 2) orthologous 2.7498 shuffled 0.4539 2.2959
Mavid (auto) orthologous 3.3181 shuffled 2.8248 0.4933
Mavid (yeast tree) orthologous 3.3393 shuffled 2.8713 0.4680
  1. Performance on the yeast benchmark of a subset of the programs in Table 1 when command-line parameters are varied. In Sigma, "no bg" indicates a background model where each nucleotide is equally probable; "no tr" indicates a "uniform" transition matrix where a nucleotide can mutate to any other nucleotide with equal probability. In FSA, "gap5" indicates the command line option --gapfactor 5. In Dialign, -1 2 is the most stringent setting. Mavid tree options are as described in the text.
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