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Table 5 SPS scores for BRAliBASE version 2.1

From: Improved accuracy of multiple ncRNA alignment by incorporating structural information into a MAFFT-based framework

   SPS
Method Time N = 2 N = 3 N = 5 N = 7 N = 10 N = 15
ClustalW (iterative) 52 minutes 0.796 0.810 0.828 0.837 0.850 0.853
ProbConsRNA 33 minutes 0.836 0.855 0.879 0.890 0.899 0.907
G-INS-i 8.8 minutes 0.837 0.851 0.874 0.890 0.901 0.913
LaRA 1.31 5.5 days 0.798 0.830 0.864 0.883 0.898 0.913
Murlet 2.5 weeks 0.843 0.863 0.886 0.897 0.906 0.915
MXSCARNA 2 4.2 hours 0.850 0.866 0.884 0.894 0.907 0.914
RNA Sampler (fast) 8.2 days 0.787 0.801 0.824 0.828 0.841 0.855
RNAsampler 2.9 weeks 0.785 0.812 0.839 0.850 0.858 0.869
X-INS-i-larapair 5.4 days 0.837 0.869 0.896 0.909 0.919 0.930
X-INS-i-scarnapair 18 hours 0.856 0.876 0.902 0.913 0.922 0.931
# of alignments   8,976 4,835 2,405 1,426 845 503
(used for Wilcoxon test)   (8,976) (4,832) (2,399) (1,420) (836) (491)
  1. The highest scores within each group (N = 2, 3, 5, 7, 10, 15) are underlined. The scores close to the highest (p > 0.01 in the Wilcoxon test) are shown in bold. As Murlet and RNA Sampler aborted for a small number of datasets, the Wilcoxon test was carried out using a limited set (the numbers of alignments are in parentheses), for which every method returned an alignment.