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Table 8 The statistical significance (i.e. p-values) of SP and TC alignment score differences between MSACompro and the other tools on three benchmark data sets.

From: MSACompro: protein multiple sequence alignment using predicted secondary structure, solvent accessibility, and residue-residue contacts

MSA tools/Score Type Whole BAliBASE SABmark OXBENCH
Clustalw/SP score < 2.2 × 10-16 < 2.2 × 10-16 < 2.2 × 10-16
Clustalw/TC score < 2.2 × 10-16 < 2.2 × 10-16 < 2.2 × 10-16
DIALIGN-TX/SP score < 2.2 × 10-16 < 2.2 × 10-16 < 2.2 × 10-16
DIALIGN-TX/TC score < 2.2 × 10-16 < 2.2 × 10-16 < 2.2 × 10-16
FSA/SP score < 2.2 × 10-16 < 2.2 × 10-16 < 2.2 × 10-16
FSA/TC score < 2.2 × 10-16 < 2.2 × 10-16 < 2.2 × 10-16
MAFFT/SP score < 2.2 × 10-16 < 2.2 × 10-16 < 2.2 × 10-16
MAFFT/TC score < 2.2 × 10-16 < 2.2 × 10-16 < 2.2 × 10-16
MSAProbs/SP score 2.931 × 10-3 < 2.2 × 10-16 < 2.2 × 10-16
MSAProbs/TC score 0.4839 < 2.2 × 10-16 < 2.2 × 10-16
MUSCLE/SP score < 2.2 × 10-16 < 2.2 × 10-16 < 2.2 × 10-16
MUSCLE/TC score < 2.2 × 10-16 < 2.2 × 10-16 < 2.2 × 10-16
Opal/SP score 3.384 × 10-16 < 2.2 × 10-16 < 2.2 × 10-16
Opal/TC score 2.15 × 10-14 < 2.2 × 10-16 < 2.2 × 10-16
POA/SP score < 2.2 × 10-16 < 2.2 × 10-16 < 2.2 × 10-16
POA/TC score < 2.2 × 10-16 < 2.2 × 10-16 < 2.2 × 10-16
Probalign/SP score 2.87 × 10-6 < 2.2 × 10-16 < 2.2 × 10-16
Probalign/TC score 4.158 × 10-3 < 2.2 × 10-16 < 2.2 × 10-16
ProbCons/SP score 2.16 × 10-15 < 2.2 × 10-16 < 2.2 × 10-16
ProbCons/TC score 6.817 × 10-7 < 2.2 × 10-16 < 2.2 × 10-16
T-coffee/SP score 1.225 × 10-14 < 2.2 × 10-16 < 2.2 × 10-16
T-coffee/TC score 4.503 × 10-8 < 2.2 × 10-16 < 2.2 × 10-16
MUMMALS/SP score 6.191 × 10-10 < 2.2 × 10-16 2.446 × 10-15
MUMMALS/TC score 8.104 × 10-5 < 2.2 × 10-16 1.265 × 10-12
PROMALS/SP score 0.0116 (-) < 2.2 × 10-16 (-) 0.0186 (-)
PROMALS/TC score 0.529 < 2.2 × 10-16 (-) 0.0274 (-)
PROMALS3D/SP score 0.0149 (-) < 2.2 × 10-16 (-) < 2.2 × 10-16 (-)
PROMALS3D/TC score 0.0078 (-) < 2.2 × 10-16 (-) < 2.2 × 10-16 (-)
  1. The p-values were calculated using the Wilcoxon matched-pair signed-rank test. All the p-values except for ones denoted by "(-)" are for hypothesis testing that MSACompro has higher alignment scores than the other methods. The p-values denoted by "(-)" are for hypothesis testing that MSACompro has lower alignment scores than the other methods.