Evaluation of the suitability of free-energy minimization using nearest-neighbor energy parameters for RNA secondary structure prediction

Table 5 Accuracy of Base-pairs Predicted with Mfold 3.1 as a Function of RNA Contact Distance^†

	16S rRNA			23S rRNA
RNA Contact Distance	496 Structures			256 Structures
Comparative	Total Base-pairs	% of Total		Total Base-pairs	% of Total
Total	191,994	100		178,958	100
2–100	145,058	76		134,085	75
2–50	121,170	63		106,534	60
51–100	23,888	12		27,551	15
101+	46,936	24		44,873	25
101–500	43,004	22		37,121	21
501+	3,932	2		7,752	4
Predicted with Mfold 3.1
Total	223,957	100		218,908	100
2–100	150,886	67		137,780	63
2–50	123,708	55		109,078	50
51–100	27,178	12		28,702	13
101+	73,071	33		81,128	37
101–500	43,498	19		44,139	20
501+	29,573	13		36,989	17
Correctly Predicted with Mfold 3.1		%C¹	%M		%C	%M
Total	81,934	43	37	77,888	44	36
2–100	75,763	52	50	67,130	50	49
2–50	64,651	53	52	54,898	52	50
51–100	11,202	47	41	12,232	44	43
101+	6,171	13	8	10,758	24	13
101–500	5,978	14	14	9,441	25	21
501+	193	5	0.7	1,317	17	4
Avg. Percent Correct ²	Current	Previous[29]		Current	Previous[30]
2–100	50	55		47	53
2–50	52	-		49	-
51–100	44	-		40	-
101–200	22	15		26	35
201–300	10	14		22	21
301–400	9	13		13	10
401–500	4	12		16	13
501+	4	-		14	-

^†All base-pairs predicted in the comparative and the Mfold optimal structure predictions including those base-pairs predicted correctly (any base-pairs with IUPAC symbols other than A,G,C, or U are excluded) are grouped by RNA contact distance for 16S and 23S rRNA. RNA contact distance is defined as the number of nucleotides intervening between the 5' and 3' halves of a base-pair. The determination of the accuracy for the structures predicted with Mfold is described in the Methods section, RNA Secondary Structure Prediction and Prediction Accuracy Calculations.
¹ %C, the percentage of comparatively predicted base-pairs; %M, the percentage of Mfold predicted base-pairs.
² The Per Sequence Average (see Per Sequence Average in Methods) percentage of comparative base-pairs in each distance category predicted correctly in the Mfold optimal structure predictions.

ISSN: 1471-2105