CompaRNA - on-line benchmarks of RNA structure prediction methods

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Metric	IPknot		RNAsubopt
MCC	0.637	>	0.540
Average MCC ± 95% Confidence Intervals	0.603 ± 0.121	>	0.517 ± 0.117
Sensitivity	0.613	>	0.571
Positive Predictive Value	0.672	>	0.522
Total TP	283	>	264
Total TN	35363	>	35278
Total FP	179	<	304
Total FP CONTRA	47	<	79
Total FP INCONS	91	<	163
Total FP COMP	41	<	62
Total FN	179	<	198
P-value	5.02343278931e-08

Comparison of performance of IPknot and RNAsubopt. 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 IPknot and RNAsubopt).
Average Matthews Correlation Coefficients (MCC) with 95% confidence intervals (CIs) were plotted for different RNA families, for which at least 3 members were present in the benchmarking dataset. 'n' denotes the number of MCCs used to calculate the average and CI. See tables below for raw data (individual counts for IPknot and RNAsubopt).
Comparison of average Matthews Correlation Coefficients (MCCs) for IPknot and RNAsubopt. 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 IPknot and RNAsubopt).

Total Scores
MCC	0.637
Average MCC ± 95% Confidence Intervals	0.603 ± 0.121
Sensitivity	0.613
Positive Predictive Value	0.672
Nr of predictions	22

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	0.33	0.55	6	517	5	1	4	0	12
2M58_A	-	0.71	0.58	0.88	7	536	1	1	0	0	5
3J0L_a	-	0.16	0.18	0.18	2	400	10	3	6	1	9
3J20_0	tRNA links to Rfam database...	0.54	0.57	0.52	12	1196	12	3	8	1	9
3J3D_C	tRNA links to Rfam database...	0.52	0.53	0.53	10	949	9	3	6	0	9
3J3E_8	5_8S_rRNA links to Rfam database...	-0.01	0.00	0.00	0	2723	25	5	14	6	15
3J3F_8	5_8S_rRNA links to Rfam database...	0.36	0.47	0.28	9	4729	40	11	12	17	10
3RKF_A	Purine links to Rfam database...	0.91	0.83	1.00	20	846	0	0	0	0	4
3SD1_A	THF links to Rfam database...	0.74	0.69	0.80	20	1508	5	0	5	0	9
3U4M_B	-	0.91	0.91	0.91	20	1254	3	2	0	1	2
3W1K_J	tRNA-Sec links to Rfam database...	0.97	0.97	0.97	30	1647	1	1	0	0	1
3W3S_B	tRNA-Sec links to Rfam database...	0.94	0.91	0.97	30	1958	2	0	1	1	3
3ZEX_C	5_8S_rRNA links to Rfam database...	0.51	0.34	0.77	10	5361	7	1	2	4	19
4A1C_2	5_8S_rRNA links to Rfam database...	0.23	0.25	0.22	5	4493	26	8	10	8	15
4AOB_A	SAM links to Rfam database...	0.50	0.48	0.54	14	1411	13	3	9	1	15
4ATO_G	-	0.49	0.57	0.44	4	211	6	0	5	1	3
4ENB_A	crcB links to Rfam database...	0.85	0.73	1.00	11	461	0	0	0	0	4
4ENC_A	crcB links to Rfam database...	0.59	0.53	0.67	8	484	4	0	4	0	7
4FRG_B	AdoCbl-variant links to Rfam database...	0.75	0.71	0.81	17	1181	4	3	1	0	7
4FRN_A	AdoCbl-variant links to Rfam database...	0.79	0.71	0.87	20	1825	3	1	2	0	8
4JF2_A	preQ1-II links to Rfam database...	0.96	0.96	0.96	23	1058	1	1	0	0	1
4JRC_A	-	0.45	0.29	0.71	5	615	2	0	2	0	12

Total Scores
MCC	0.540
Average MCC ± 95% Confidence Intervals	0.517 ± 0.117
Sensitivity	0.571
Positive Predictive Value	0.522
Nr of predictions	22

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...	-0.03	0.00	0.00	0	513	15	3	12	0	18
2M58_A	-	0.60	0.58	0.64	7	533	4	1	3	0	5
3J0L_a	-	0.35	0.36	0.36	4	400	8	3	4	1	7
3J20_0	tRNA links to Rfam database...	0.51	0.57	0.48	12	1194	14	2	11	1	9
3J3D_C	tRNA links to Rfam database...	0.65	0.74	0.58	14	944	10	5	5	0	5
3J3E_8	5_8S_rRNA links to Rfam database...	0.25	0.33	0.20	5	2717	32	7	13	12	10
3J3F_8	5_8S_rRNA links to Rfam database...	0.35	0.47	0.26	9	4726	42	13	13	16	10
3RKF_A	Purine links to Rfam database...	0.91	0.83	1.00	20	846	0	0	0	0	4
3SD1_A	THF links to Rfam database...	0.73	0.72	0.75	21	1505	7	4	3	0	8
3U4M_B	-	0.49	0.55	0.46	12	1250	14	3	11	0	10
3W1K_J	tRNA-Sec links to Rfam database...	0.97	0.97	0.97	30	1647	1	1	0	0	1
3W3S_B	tRNA-Sec links to Rfam database...	0.95	0.94	0.97	31	1957	2	0	1	1	2
3ZEX_C	5_8S_rRNA links to Rfam database...	0.30	0.34	0.26	10	5336	43	5	23	15	19
4A1C_2	5_8S_rRNA links to Rfam database...	0.18	0.25	0.14	5	4481	43	13	17	13	15
4AOB_A	SAM links to Rfam database...	0.62	0.62	0.64	18	1409	11	4	6	1	11
4ATO_G	-	0.36	0.43	0.33	3	211	6	6	0	0	4
4ENB_A	crcB links to Rfam database...	0.85	0.73	1.00	11	461	2	0	0	2	4
4ENC_A	crcB links to Rfam database...	0.36	0.33	0.42	5	484	7	0	7	0	10
4FRG_B	AdoCbl-variant links to Rfam database...	0.36	0.38	0.38	9	1178	15	2	13	0	15
4FRN_A	AdoCbl-variant links to Rfam database...	0.58	0.57	0.59	16	1821	11	3	8	0	12
4JF2_A	preQ1-II links to Rfam database...	0.69	0.67	0.73	16	1060	6	4	2	0	8
4JRC_A	-	0.34	0.35	0.35	6	605	11	0	11	0	11

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