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

Table 3

A comparison of the highest matching base pair structures from SARNA-predict, RnaPredict, ACRNA, PAF, PSOfold, and mfold in terms of sensitivity and specificity.

Sequence	Length	SARNA-Predict		RnaPredict		ACRNA		PAF		PSOfold		mfold
		Se	Sp	Se	Sp	Se	Sp	Se	Sp	Se	Sp	Se	Sp
D. virilis	784	42.1	42.2	27.9	26.9	27.9	26.9	44.2	41.7	42.9	41.5	35.2	32.5
X. laevis	945	46.2	48.9	37.1	38.8	45.8	46.9	46.2	49.4	45.6	48.5	45.0	46.1
H. marismortui	122	71.1	90.0	71.1	90.0	76.3	78.4	73.7	90.3	71.1	87.1	76.3	85.3
A. lagunensis	468	74.3	64.6	60.2	51.9	63.7	54.1	75.2	68.6	76.1	64.7	65.5	55.6
M. anisopliae var.	394	63.3	65.0	62.5	62.0	63.3	65.0	75.8	82.7	75.0	74.4	76.7	79.3
H. rubra	543	64.5	56.7	57.2	49.1	58.0	47.9	59.4	58.1	58.0	53.0	60.1	49.7
A. griffini	556	74.0	58.8	61.8	50.3	73.3	55.2	77.9	63.8	76.3	59.2	72.5	54.6
H. sapiens	954	44.7	48.8	33.5	35.6	44.7	48.8	46.6	47.7	44.4	47.2	35.7	36.8
A. fulgens	964	35.1	38.9	30.9	33.9	34.3	38.7	37.4	39.8	35.1	39.6	27.9	30.7
S. acidocaldarius	1494	52.4	51.9	52.4	51.9	58.3	58.0	60	58.1	58.3	58.0	57.9	54.6
Averages	722.4	56.77	56.58	49.46	49.04	54.56	51.99	59.64	60.02	58.28	57.32	55.28	52.52