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Table 4 Variances of specificity, sensitivity, accuracy, and MCC for both 5p and 3p arms by five-fold cross-validation using PHDCleav and LBSizeCleav (k=1,,5) with window sizes 8,10,12,14 based on sequences and secondary structures predicted by quikfold server

From: LBSizeCleav: improved support vector machine (SVM)-based prediction of Dicer cleavage sites using loop/bulge length

feature extraction method Window size CD-5p CD-3p
   Sn Sp Ac Mc Sn Sp Ac Mc
PHDCleav (sequence) 8 0.0137 0.0008 0.0074 0.0036 0.0072 0.0015 0.0094 0.0066
  10 0.0184 0.0004 0.0111 0.0018 0.0044 0.0005 0.0072 0.0024
  12 0.0208 0.0001 0.0223 0.0003 0.0078 0.0011 0.0031 0.0046
  14 0.0293 0.0009 0.0174 0.0037 0.0065 0.0007 0.0048 0.0029
PHDCleav (structure) 8 0.0042 0.0039 0.0067 0.0155 0.0187 0.0013 0.0091 0.0062
  10 0.0026 0.0043 0.0088 0.0177 0.0100 0.0014 0.0050 0.0059
  12 0.0042 0.0027 0.0034 0.0109 0.0051 0.0011 0.0024 0.0045
  14 0.0047 0.0031 0.0034 0.0125 0.0039 0.0012 0.0014 0.0047
Extended PHDCleav 8 0.0029 0.0032 0.0063 0.0128 0.0123 0.0025 0.0043 0.0103
  10 0.0030 0.0038 0.0061 0.0154 0.0064 0.0019 0.0016 0.0075
  12 0.0040 0.0033 0.0050 0.0136 0.0054 0.0015 0.0011 0.0059
  14 0.0059 0.0027 0.0016 0.0108 0.0032 0.0013 0.0010 0.0052
LBSizeCleav (k=1) 8 0.0030 0.0025 0.0044 0.0115 0.0100 0.0004 0.0074 0.0019
  10 0.0022 0.0015 0.0013 0.0064 0.0078 0.0011 0.0015 0.0042
  12 0.0050 0.0024 0.0010 0.0090 0.0077 0.0015 0.0002 0.0051
  14 0.0075 0.0035 0.0010 0.0132 0.0036 0.0007 0.0002 0.0026
LBSizeCleav (k=2) 8 0.0042 0.0018 0.0008 0.0066 0.0053 0.0010 0.0036 0.0041
  10 0.0038 0.0020 0.0009 0.0076 0.0034 0.0010 0.0010 0.0039
  12 0.0051 0.0029 0.0016 0.0115 0.0042 0.0017 0.0008 0.0063
  14 0.0051 0.0028 0.0012 0.0107 0.0043 0.0008 0.0002 0.0024
LBSizeCleav (k=3) 8 0.0025 0.0013 0.0008 0.0050 0.0070 0.0010 0.0021 0.0042
  10 0.0039 0.0022 0.0012 0.0086 0.0064 0.0013 0.0006 0.0048
  12 0.0063 0.0031 0.0012 0.0119 0.0039 0.0015 0.0005 0.0055
  14 0.0060 0.0033 0.0015 0.0130 0.0073 0.0016 0.0003 0.0046
LBSizeCleav (k=4) 8 0.0029 0.0016 0.0009 0.0064 0.0066 0.0020 0.0030 0.0078
  10 0.0046 0.0025 0.0011 0.0095 0.0071 0.0014 0.0006 0.0049
  12 0.0061 0.0032 0.0014 0.0124 0.0033 0.0011 0.0007 0.0041
  14 0.0051 0.0030 0.0015 0.0120 0.0088 0.0025 0.0002 0.0082
LBSizeCleav (k=5) 8 0.0029 0.0017 0.0009 0.0066 0.0062 0.0021 0.0031 0.0082
  10 0.0055 0.0029 0.0013 0.0113 0.0032 0.0011 0.0005 0.0042
  12 0.0051 0.0029 0.0015 0.0114 0.0029 0.0011 0.0009 0.0044
  14 0.0047 0.0029 0.0016 0.0116 0.0076 0.0023 0.0002 0.0076
  1. Sn, Sp, Ac, and MCC denote sensitivity, specificity, accuracy, and Matthews correlation coefficient, respectively
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