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Table 2 Results on average 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

Method Window size 5p arm 3p arm
   Sn Sp Ac MCC Sn Sp Ac MCC
PHDCleav (sequence) 8 0.602 0.503 0.552 0.105 0.662 0.625 0.644 0.287
  10 0.541 0.573 0.557 0.115 0.661 0.642 0.652 0.303
  12 0.560 0.555 0.557 0.115 0.660 0.656 0.658 0.316
  14 0.539 0.572 0.555 0.111 0.654 0.702 0.678 0.356
PHDCleav (structure) 8 0.753 0.814 0.784 0.568 0.670 0.661 0.665 0.330
  10 0.784 0.827 0.806 0.612 0.702 0.719 0.710 0.421
  12 0.790 0.842 0.816 0.633 0.739 0.764 0.752 0.503
  14 0.799 0.857 0.828 0.657 0.779 0.783 0.781 0.562
Extended PHDCleav 8 0.750 0.798 0.774 0.548 0.652 0.716 0.684 0.369
  10 0.779 0.827 0.803 0.607 0.674 0.783 0.729 0.460
  12 0.809 0.845 0.827 0.654 0.714 0.790 0.752 0.506
  14 0.813 0.868 0.840 0.682 0.781 0.801 0.791 0.582
LBSizeCleav (k=1) 8 0.668 0.924 0.796 0.612 0.630 0.684 0.657 0.315
  10 0.709 0.947 0.828 0.675 0.651 0.776 0.713 0.430
  12 0.774 0.945 0.859 0.730 0.686 0.847 0.766 0.540
  14 0.808 0.933 0.871 0.747 0.758 0.874 0.816 0.637
LBSizeCleav (k=2) 8 0.662 0.954 0.808 0.645 0.626 0.723 0.674 0.351
  10 0.725 0.946 0.835 0.688 0.642 0.806 0.724 0.455
  12 0.784 0.938 0.861 0.731 0.665 0.882 0.773 0.560
  14 0.820 0.925 0.872 0.749 0.734 0.916 0.825 0.661
LBSizeCleav (k=3) 8 0.692 0.949 0.821 0.664 0.619 0.735 0.677 0.356
  10 0.752 0.941 0.846 0.706 0.618 0.822 0.720 0.450
  12 0.803 0.932 0.867 0.741 0.635 0.914 0.774 0.571
  14 0.825 0.912 0.869 0.740 0.719 0.942 0.830 0.678
LBSizeCleav (k=4) 8 0.695 0.949 0.822 0.667 0.614 0.736 0.675 0.353
  10 0.767 0.938 0.853 0.716 0.621 0.835 0.728 0.467
  12 0.815 0.927 0.871 0.747 0.639 0.912 0.776 0.573
  14 0.835 0.909 0.872 0.746 0.723 0.924 0.823 0.660
LBSizeCleav (k=5) 8 0.700 0.947 0.824 0.668 0.594 0.771 0.682 0.371
  10 0.772 0.936 0.854 0.717 0.578 0.862 0.720 0.459
  12 0.821 0.924 0.872 0.749 0.634 0.921 0.777 0.579
  14 0.838 0.909 0.874 0.749 0.724 0.932 0.828 0.671
  1. Sn, Sp, Ac, and MCC denote sensitivity, specificity, accuracy, and Matthews correlation coefficient, respectively