CompaRNA - on-line benchmarks of RNA structure prediction methods

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Metric	IPknot		Alterna
MCC	0.791	>	0.684
Average MCC ± 95% Confidence Intervals	0.773 ± 0.149	>	0.695 ± 0.147
Sensitivity	0.754	>	0.705
Positive Predictive Value	0.840	>	0.679
Total TP	199	>	186
Total TN	10337	>	10300
Total FP	59	<	115
Total FP CONTRA	9	<	27
Total FP INCONS	29	<	61
Total FP COMP	21	<	27
Total FN	65	<	78
P-value	5.19332990918e-08

Comparison of performance of IPknot and Alterna. 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 Alterna).
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 Alterna).
Comparison of average Matthews Correlation Coefficients (MCCs) for IPknot and Alterna. 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 Alterna).

Total Scores
MCC	0.791
Average MCC ± 95% Confidence Intervals	0.773 ± 0.149
Sensitivity	0.754
Positive Predictive Value	0.840
Nr of predictions	22

RNA Chain	Rfam family	MCC	SENS	PPV	TP	TN	FP	FP CONTRA	FP INCONS	FP COMP	FN
2LBS_A	-	1.00	1.00	1.00	14	193	0	0	0	0	0
2LC8_A	GP_knot1 links to Rfam database...	0.41	0.33	0.55	6	517	5	1	4	0	12
2LDL_A	-	1.00	1.00	1.00	9	131	0	0	0	0	0
2LDT_A	-	1.00	1.00	1.00	11	151	0	0	0	0	0
2LK3_A	-	1.00	1.00	1.00	9	91	0	0	0	0	0
2YIE_Z	-	0.53	0.63	0.45	5	591	6	4	2	0	3
2YIE_X	-	1.00	1.00	1.00	7	537	3	0	0	3	0
3AMU_B	tRNA links to Rfam database...	0.81	0.79	0.83	15	1139	6	0	3	3	4
3J0L_a	-	0.16	0.18	0.18	2	400	10	3	6	1	9
3J0L_8	-	1.00	1.00	1.00	7	69	0	0	0	0	0
3J0L_1	-	0.83	0.77	0.91	10	473	4	0	1	3	3
3J0L_7	-	-0.02	0.00	0.00	0	512	7	1	6	0	10
3J0L_g	-	-0.01	0.00	0.00	0	174	4	0	2	2	2
3J16_L	tRNA links to Rfam database...	0.90	0.81	1.00	17	1142	0	0	0	0	4
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
3SIU_F	-	0.86	0.75	1.00	6	139	0	0	0	0	2
3SN2_B	IRE_II links to Rfam database...	0.95	0.92	1.00	11	143	0	0	0	0	1
3TRZ_Z	-	1.00	1.00	1.00	5	87	1	0	0	1	0
3TS0_U	-	1.00	1.00	1.00	6	112	1	0	0	1	0
3TS2_V	-	1.00	1.00	1.00	5	103	0	0	0	0	0
3UZL_B	tRNA links to Rfam database...	0.93	0.88	1.00	14	1279	7	0	0	7	2

Total Scores
MCC	0.684
Average MCC ± 95% Confidence Intervals	0.695 ± 0.147
Sensitivity	0.705
Positive Predictive Value	0.679
Nr of predictions	22

RNA Chain	Rfam family	MCC	SENS	PPV	TP	TN	FP	FP CONTRA	FP INCONS	FP COMP	FN
2LBS_A	-	1.00	1.00	1.00	14	193	0	0	0	0	0
2LC8_A	GP_knot1 links to Rfam database...	0.47	0.44	0.53	8	513	7	0	7	0	10
2LDL_A	-	1.00	1.00	1.00	9	131	1	0	0	1	0
2LDT_A	-	1.00	1.00	1.00	11	151	0	0	0	0	0
2LK3_A	-	1.00	1.00	1.00	9	91	0	0	0	0	0
2YIE_Z	-	-0.02	0.00	0.00	0	587	15	6	9	0	8
2YIE_X	-	0.53	0.57	0.50	4	536	9	1	3	5	3
3AMU_B	tRNA links to Rfam database...	0.73	0.79	0.68	15	1135	10	0	7	3	4
3J0L_a	-	0.18	0.18	0.22	2	402	8	3	4	1	9
3J0L_8	-	1.00	1.00	1.00	7	69	0	0	0	0	0
3J0L_1	-	0.63	0.62	0.67	8	472	8	0	4	4	5
3J0L_7	-	0.37	0.40	0.36	4	508	9	2	5	2	6
3J0L_g	-	-0.02	0.00	0.00	0	169	9	3	4	2	2
3J16_L	tRNA links to Rfam database...	0.76	0.76	0.76	16	1138	5	3	2	0	5
3RKF_A	Purine links to Rfam database...	0.82	0.79	0.86	19	844	3	1	2	0	5
3SD1_A	THF links to Rfam database...	0.55	0.55	0.57	16	1505	12	4	8	0	13
3SIU_F	-	0.69	0.75	0.67	6	136	3	0	3	0	2
3SN2_B	IRE_II links to Rfam database...	0.91	0.83	1.00	10	144	0	0	0	0	2
3TRZ_Z	-	1.00	1.00	1.00	5	87	2	0	0	2	0
3TS0_U	-	1.00	1.00	1.00	6	112	1	0	0	1	0
3TS2_V	-	1.00	1.00	1.00	5	103	0	0	0	0	0
3UZL_B	tRNA links to Rfam database...	0.68	0.75	0.63	12	1274	13	4	3	6	4

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