A Novel Framework Based on ACO and PSO for RNA Secondary Structure Prediction

Table 2

A comparison of the highest matching base pair structures from PAF and mfold in terms of sensitivity, specificity, and 𝐹-measure.

Sequence	Known bps	Predicted bps		TP		FP		FN		Sensitivity		Specificity		𝐹-measure
		PAF	mfold	PAF	mfold	PAF	mfold	PAF	mfold	PAF	mfold	PAF	mfold	PAF	mfold
D. virilis	233	247	252	103	82	144	170	130	151	44.2	35.2	41.7	32.5	42.9	33.8
X. laevis	251	235	245	116	113	119	132	135	138	46.2	45.0	49.4	46.1	47.7	45.6
H. marismortui	38	31	34	28	29	3	5	10	9	73.7	76.3	90.3	85.3	81.2	80.6
A. lagunensis	113	124	133	85	74	39	59	28	39	75.2	65.5	68.6	55.6	71.7	60.2
M. anisopliae var.	120	110	116	91	92	19	24	29	28	75.8	76.7	82.7	79.3	79.1	78.0
H. rubra	138	141	167	82	83	59	84	56	55	59.4	60.1	58.1	49.7	58.8	54.4
A. griffini	131	160	174	102	95	58	79	29	36	77.9	72.5	63.8	54.6	70.1	62.3
H. sapiens	266	260	258	124	95	136	163	142	171	46.6	35.7	47.7	36.8	47.2	36.3
A. fulgens	265	249	241	99	74	150	167	166	191	37.4	27.9	39.8	30.7	38.5	29.2
S. acidocaldarius	468	483	496	281	271	202	225	187	197	60	57.9	58.1	54.6	59.1	56.2
Averages	202.3	204	211.6	111.1	100.8	92.9	110.8	91.2	101.5	59.64	55.28	60.02	52.52	59.63	53.66