CompaRNA - on-line benchmarks of RNA structure prediction methods

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Metric	UNAFold		RDfolder
MCC	0.704	>	0.549
Average MCC ± 95% Confidence Intervals	0.663 ± 0.145	>	0.543 ± 0.164
Sensitivity	0.685	>	0.487
Positive Predictive Value	0.737	>	0.640
Total TP	283	>	201
Total TN	17904	<	17974
Total FP	109	<	115
Total FP CONTRA	32	>	22
Total FP INCONS	69	<	91
Total FP COMP	8	>	2
Total FN	130	<	212
P-value	5.10776592382e-08

Comparison of performance of UNAFold and RDfolder. 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 UNAFold and RDfolder).
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 UNAFold and RDfolder).
Comparison of average Matthews Correlation Coefficients (MCCs) for UNAFold and RDfolder. 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 UNAFold and RDfolder).

Total Scores
MCC	0.704
Average MCC ± 95% Confidence Intervals	0.663 ± 0.145
Sensitivity	0.685
Positive Predictive Value	0.737
Nr of predictions	20

RNA Chain	Rfam family	MCC	SENS	PPV	TP	TN	FP	FP CONTRA	FP INCONS	FP COMP	FN
2KFC_A	-	-0.03	0.00	0.00	0	229	7	1	6	0	8
2LC8_A	GP_knot1 links to Rfam database...	-0.03	0.00	0.00	0	513	15	3	12	0	18
2RP0_A	-	0.84	0.71	1.00	5	111	0	0	0	0	2
2ZZN_D	tRNA links to Rfam database...	0.93	0.95	0.91	21	961	2	2	0	0	1
3A2K_C	tRNA links to Rfam database...	0.47	0.50	0.46	11	1084	13	3	10	0	11
3A3A_A	tRNA-Sec links to Rfam database...	0.97	0.93	1.00	28	1472	0	0	0	0	2
3ADB_C	-	0.86	0.85	0.88	28	1787	4	0	4	0	5
3GCA_A	-	0.84	0.71	1.00	5	153	0	0	0	0	2
3GX2_A	SAM links to Rfam database...	0.81	0.79	0.85	22	1423	5	2	2	1	6
3IVN_B	Purine links to Rfam database...	0.91	0.83	1.00	19	884	0	0	0	0	4
3IWN_A	c-di-GMP-I links to Rfam database...	0.80	0.79	0.81	22	1445	6	1	4	1	6
3J0L_a	-	0.55	0.64	0.50	7	397	8	5	2	1	4
3JYV_7	tRNA links to Rfam database...	0.24	0.25	0.25	5	1091	16	7	8	1	15
3LA5_A	Purine links to Rfam database...	0.91	0.84	1.00	21	933	0	0	0	0	4
3NKB_B	-	0.69	0.74	0.67	14	714	7	0	7	0	5
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...	0.77	0.76	0.79	22	1505	6	4	2	0	7
4AOB_A	SAM links to Rfam database...	0.60	0.59	0.63	17	1410	11	4	6	1	12
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...	0.37	0.33	0.45	5	485	7	0	6	1	10

Total Scores
MCC	0.549
Average MCC ± 95% Confidence Intervals	0.543 ± 0.164
Sensitivity	0.487
Positive Predictive Value	0.640
Nr of predictions	20

RNA Chain	Rfam family	MCC	SENS	PPV	TP	TN	FP	FP CONTRA	FP INCONS	FP COMP	FN
2KFC_A	-	0.79	0.63	1.00	5	231	0	0	0	0	3
2LC8_A	GP_knot1 links to Rfam database...	-0.03	0.00	0.00	0	514	14	3	11	0	18
2RP0_A	-	0.84	0.71	1.00	5	111	0	0	0	0	2
2ZZN_D	tRNA links to Rfam database...	0.93	0.95	0.91	21	961	2	2	0	0	1
3A2K_C	tRNA links to Rfam database...	0.98	0.95	1.00	21	1087	0	0	0	0	1
3A3A_A	tRNA-Sec links to Rfam database...	0.59	0.50	0.71	15	1479	6	0	6	0	15
3ADB_C	-	0.48	0.45	0.54	15	1791	13	1	12	0	18
3GCA_A	-	0.84	0.71	1.00	5	153	0	0	0	0	2
3GX2_A	SAM links to Rfam database...	0.60	0.57	0.64	16	1424	10	2	7	1	12
3IVN_B	Purine links to Rfam database...	0.91	0.83	1.00	19	884	0	0	0	0	4
3IWN_A	c-di-GMP-I links to Rfam database...	-0.01	0.00	0.00	0	1462	10	1	9	0	28
3J0L_a	-	-0.02	0.00	0.00	0	407	4	3	1	0	11
3JYV_7	tRNA links to Rfam database...	-0.02	0.00	0.00	0	1091	20	4	16	0	20
3LA5_A	Purine links to Rfam database...	0.91	0.84	1.00	21	933	0	0	0	0	4
3NKB_B	-	0.43	0.42	0.47	8	718	9	2	7	0	11
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...	0.35	0.24	0.54	7	1520	6	1	5	0	22
4AOB_A	SAM links to Rfam database...	0.42	0.38	0.48	11	1414	13	3	9	1	18
4ENB_A	crcB links to Rfam database...	0.48	0.40	0.60	6	462	4	0	4	0	9
4ENC_A	crcB links to Rfam database...	0.48	0.40	0.60	6	486	4	0	4	0	9

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