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Table 3 Evaluation of predictive accuracy TP = true positives, sens. = sensitivity, FP = false positives, sel. = selectivity, K = (number of correct predicted pseudoknot helices)/ (expected number of pseudoknot helices). False negatives can be derived from: FN = BPTP. For HIVRT, PseudoBase and tRNA the average over all sequences is taken.

From: Design, implementation and evaluation of a practical pseudoknot folding algorithm based on thermodynamics

   RNAfold pknotsRE pknotsRG-mfe
Sequence BP TP(sens.) FP(sel.) K TP(sens.) FP(sel.) K TP(sens.) FP(sel.) K
PseudoBase 13.1 7.1(54.2) 4.4(61.9) - 9.2(72.3) 3.8(70.7) - 10.2(77.3) 3.5(74.7) -
HIVRT 11 4.7(42.8) 1.7(73.3) 1/2 11(100) 0(100) 2/2 11(100) 0(100) 2/2
tRNAs 18.7 9.4(50.4) 12.5(43.0) 0/0 - - - 9.8(52.3) 12.2(44.5) 0/0
HDV 32 12(37.5) 16(42.9) 2/4 14(43.8) 16(46.7) 2/4 29(90.6) 2(93.5) 3/4
ag-HDV 25 4(16.0) 24(14.3) 1/2 24(96.0) 9(72.7) 2/2 21(84.0) 11(65.6) 2/2
TYMV 24 17(70.8) 6(73.9) 1/2 24(100) 1(96.0) 2/2 23(95.8) 2(92.0) 2/2
TMV 25 13(52.0) 8(61.9) 3/6 13(52.0) 9(59.1) 3/6 20(80.0) 4(83.3) 6/6
STNV 69 26(37.7) 54(32.5) 2/8 - - - 42(60.9) 37(53.2) 5/8