CompaRNA - on-line benchmarks of RNA structure prediction methods

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Metric	RNASLOpt		MCFold
MCC	0.461	>	0.441
Average MCC ± 95% Confidence Intervals	0.416 ± 0.166	>	0.380 ± 0.179
Sensitivity	0.393	<	0.474
Positive Predictive Value	0.550	>	0.419
Total TP	126	<	152
Total TN	43907	>	43773
Total FP	112	<	247
Total FP CONTRA	13	<	36
Total FP INCONS	90	<	175
Total FP COMP	9	<	36
Total FN	195	>	169
P-value	2.14792285362e-08

Comparison of performance of RNASLOpt and MCFold. Positive Predictive Value (PPV) is plotted against sensitivity. Each dot represents a single test of each method. See tables below for raw data (individual counts for RNASLOpt and MCFold).
Comparison of average Matthews Correlation Coefficients (MCCs) for RNASLOpt and MCFold. The whiskers correspond to 95% confidence intervals (CIs). 'n' denotes the number of MCCs used to calculate average MCCs and CIs. See tables below for raw data (individual counts for RNASLOpt and MCFold).

Total Scores
MCC	0.461
Average MCC ± 95% Confidence Intervals	0.416 ± 0.166
Sensitivity	0.393
Positive Predictive Value	0.550
Nr of predictions	12

RNA Chain	Rfam family	MCC	SENS	PPV	TP	TN	FP	FP CONTRA	FP INCONS	FP COMP	FN
2LC8_A	GP_knot1 links to Rfam database...	0.47	0.35	0.64	7	1529	4	0	4	0	13
2LKR_A	-	0.68	0.62	0.75	24	6073	9	0	8	1	15
3J0L_7	-	-0.01	0.00	0.00	0	1212	13	0	13	0	17
3J0L_a	-	0.26	0.19	0.38	3	1120	5	1	4	0	13
3J0L_g	-	-0.01	0.00	0.00	0	461	4	1	3	0	4
3J0L_2	-	0.39	0.36	0.43	12	6188	18	2	14	2	21
3J16_L	tRNA links to Rfam database...	0.53	0.40	0.71	12	2758	5	0	5	0	18
3U4M_B	-	0.38	0.32	0.46	12	3134	14	0	14	0	25
4A1C_2	5_8S_rRNA links to Rfam database...	0.23	0.24	0.22	8	11744	35	8	21	6	25
4A1C_3	5S_rRNA links to Rfam database...	0.67	0.52	0.88	28	7108	4	0	4	0	26
4ENB_A	crcB links to Rfam database...	0.76	0.58	1.00	11	1264	0	0	0	0	8
4ENC_A	crcB links to Rfam database...	0.65	0.47	0.90	9	1316	1	1	0	0	10

Total Scores
MCC	0.441
Average MCC ± 95% Confidence Intervals	0.380 ± 0.179
Sensitivity	0.474
Positive Predictive Value	0.419
Nr of predictions	12

RNA Chain	Rfam family	MCC	SENS	PPV	TP	TN	FP	FP CONTRA	FP INCONS	FP COMP	FN
2LC8_A	GP_knot1 links to Rfam database...	0.41	0.45	0.39	9	1517	16	0	14	2	11
2LKR_A	-	0.93	0.92	0.95	36	6067	14	0	2	12	3
3J0L_7	-	-0.01	0.00	0.00	0	1206	19	4	15	0	17
3J0L_a	-	0.16	0.19	0.17	3	1110	15	1	14	0	13
3J0L_g	-	0.13	0.25	0.08	1	452	12	8	4	0	3
3J0L_2	-	0.21	0.24	0.18	8	6172	39	7	29	3	25
3J16_L	tRNA links to Rfam database...	0.45	0.47	0.44	14	2743	19	1	17	1	16
3U4M_B	-	0.59	0.59	0.59	22	3123	15	0	15	0	15
4A1C_2	5_8S_rRNA links to Rfam database...	0.13	0.15	0.11	5	11735	56	10	31	15	28
4A1C_3	5S_rRNA links to Rfam database...	0.68	0.67	0.71	36	7089	17	1	14	2	18
4ENB_A	crcB links to Rfam database...	0.61	0.63	0.60	12	1255	8	2	6	0	7
4ENC_A	crcB links to Rfam database...	0.28	0.32	0.27	6	1304	17	2	14	1	13

Matthews Correlation Coeffient, Sensitivity and Positive Predictive Value have been calculated based on the paper by Gardener & Giegerich, 2004.