CompaRNA - on-line benchmarks of RNA structure prediction methods

FAQ

Metric	MCFold		RNAwolf
MCC	0.449	>	0.390
Average MCC ± 95% Confidence Intervals	0.403 ± 0.146	>	0.367 ± 0.136
Sensitivity	0.474	>	0.366
Positive Predictive Value	0.434	>	0.425
Total TP	201	>	155
Total TN	52803	<	52901
Total FP	298	>	229
Total FP CONTRA	39	>	26
Total FP INCONS	223	>	184
Total FP COMP	36	>	19
Total FN	223	<	269
P-value	2.1413769576e-08

Comparison of performance of MCFold and RNAwolf. 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 MCFold and RNAwolf).
Comparison of average Matthews Correlation Coefficients (MCCs) for MCFold and RNAwolf. 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 MCFold and RNAwolf).

Total Scores
MCC	0.449
Average MCC ± 95% Confidence Intervals	0.403 ± 0.146
Sensitivity	0.474
Positive Predictive Value	0.434
Nr of predictions	15

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
3AMU_B	tRNA links to Rfam database...	0.44	0.48	0.42	13	2972	18	2	16	0	14
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
3J0L_a	-	0.16	0.19	0.17	3	1110	15	1	14	0	13
3J0L_7	-	-0.01	0.00	0.00	0	1206	19	4	15	0	17
3J16_L	tRNA links to Rfam database...	0.45	0.47	0.44	14	2743	19	1	17	1	16
3RKF_A	Purine links to Rfam database...	0.70	0.65	0.76	22	2182	7	1	6	0	12
3SD1_A	THF links to Rfam database...	0.33	0.33	0.35	14	3876	26	0	26	0	28
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

Total Scores
MCC	0.390
Average MCC ± 95% Confidence Intervals	0.367 ± 0.136
Sensitivity	0.366
Positive Predictive Value	0.425
Nr of predictions	15

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...	0.52	0.50	0.56	10	1522	8	0	8	0	10
2LKR_A	-	0.81	0.74	0.88	29	6072	8	0	4	4	10
3AMU_B	tRNA links to Rfam database...	0.68	0.63	0.74	17	2980	9	0	6	3	10
3J0L_g	-	0.16	0.25	0.11	1	456	8	6	2	0	3
3J0L_2	-	0.11	0.12	0.11	4	6181	34	5	26	3	29
3J0L_a	-	0.18	0.19	0.20	3	1113	12	1	11	0	13
3J0L_7	-	-0.01	0.00	0.00	0	1214	11	0	11	0	17
3J16_L	tRNA links to Rfam database...	0.45	0.40	0.52	12	2752	11	0	11	0	18
3RKF_A	Purine links to Rfam database...	0.72	0.62	0.84	21	2186	4	0	4	0	13
3SD1_A	THF links to Rfam database...	0.46	0.43	0.50	18	3880	18	0	18	0	24
3U4M_B	-	0.44	0.38	0.52	14	3133	13	0	13	0	23
4A1C_2	5_8S_rRNA links to Rfam database...	0.08	0.09	0.08	3	11741	46	10	27	9	30
4A1C_3	5S_rRNA links to Rfam database...	0.23	0.20	0.28	11	7101	28	2	26	0	43
4ENB_A	crcB links to Rfam database...	0.35	0.32	0.40	6	1260	9	1	8	0	13
4ENC_A	crcB links to Rfam database...	0.34	0.32	0.38	6	1310	10	1	9	0	13

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