CompaRNA - on-line benchmarks of RNA structure prediction methods

FAQ

Metric	Pknots		RNASLOpt
MCC	0.568	>	0.558
Average MCC ± 95% Confidence Intervals	0.586 ± 0.146	>	0.547 ± 0.139
Sensitivity	0.609	>	0.555
Positive Predictive Value	0.541	<	0.572
Total TP	249	>	227
Total TN	32925	<	32988
Total FP	269	>	227
Total FP CONTRA	73	=	73
Total FP INCONS	138	>	97
Total FP COMP	58	>	57
Total FN	160	<	182
P-value	0.00371712387624

Comparison of performance of Pknots and RNASLOpt. 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 Pknots and RNASLOpt).
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 Pknots and RNASLOpt).
Comparison of average Matthews Correlation Coefficients (MCCs) for Pknots and RNASLOpt. 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 Pknots and RNASLOpt).

Total Scores
MCC	0.568
Average MCC ± 95% Confidence Intervals	0.586 ± 0.146
Sensitivity	0.609
Positive Predictive Value	0.541
Nr of predictions	20

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...	0.83	0.83	0.83	15	510	3	2	1	0	3
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...	0.95	0.95	0.95	20	1198	2	1	0	1	1
3J3D_C	tRNA links to Rfam database...	0.46	0.53	0.42	10	944	14	5	9	0	9
3J3E_8	5_8S_rRNA links to Rfam database...	0.10	0.13	0.09	2	2720	33	5	15	13	13
3J3F_8	5_8S_rRNA links to Rfam database...	0.42	0.53	0.33	10	4731	37	10	10	17	9
3U4M_B	-	0.33	0.36	0.32	8	1251	17	4	13	0	14
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...	0.78	0.76	0.81	25	1958	7	1	5	1	8
3ZEX_C	5_8S_rRNA links to Rfam database...	0.10	0.14	0.08	4	5322	54	13	35	6	25
4A1C_2	5_8S_rRNA links to Rfam database...	0.33	0.40	0.29	8	4488	36	9	11	16	12
4AOB_A	SAM links to Rfam database...	0.19	0.21	0.21	6	1409	23	3	19	1	23
4ATO_G	-	0.36	0.43	0.33	3	211	6	6	0	0	4
4ENB_A	crcB links to Rfam database...	1.00	1.00	1.00	15	457	2	0	0	2	0
4ENC_A	crcB links to Rfam database...	0.97	1.00	0.94	15	480	1	1	0	0	0
4FRG_B	AdoCbl-variant links to Rfam database...	0.55	0.50	0.63	12	1183	7	0	7	0	12
4FRN_A	AdoCbl-variant links to Rfam database...	0.57	0.54	0.63	15	1824	9	3	6	0	13
4JF2_A	preQ1-II links to Rfam database...	0.92	1.00	0.86	24	1054	4	4	0	0	0
4JRC_A	-	0.94	0.94	0.94	16	605	1	1	0	0	1

Total Scores
MCC	0.558
Average MCC ± 95% Confidence Intervals	0.547 ± 0.139
Sensitivity	0.555
Positive Predictive Value	0.572
Nr of predictions	20

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...	0.48	0.39	0.64	7	517	4	0	4	0	11
2M58_A	-	0.37	0.33	0.44	4	535	5	4	1	0	8
3J0L_a	-	0.21	0.18	0.29	2	404	6	3	2	1	9
3J20_0	tRNA links to Rfam database...	0.74	0.76	0.73	16	1197	7	3	3	1	5
3J3D_C	tRNA links to Rfam database...	0.90	0.95	0.86	18	947	3	3	0	0	1
3J3E_8	5_8S_rRNA links to Rfam database...	-0.01	0.00	0.00	0	2724	30	6	12	12	15
3J3F_8	5_8S_rRNA links to Rfam database...	0.39	0.47	0.32	9	4733	38	10	9	19	10
3U4M_B	-	0.49	0.55	0.46	12	1250	14	3	11	0	10
3W1K_J	tRNA-Sec links to Rfam database...	0.93	0.90	0.97	28	1649	1	1	0	0	3
3W3S_B	tRNA-Sec links to Rfam database...	0.90	0.85	0.97	28	1960	2	0	1	1	5
3ZEX_C	5_8S_rRNA links to Rfam database...	0.32	0.34	0.31	10	5342	36	8	14	14	19
4A1C_2	5_8S_rRNA links to Rfam database...	0.30	0.40	0.24	8	4482	35	13	13	9	12
4AOB_A	SAM links to Rfam database...	0.31	0.28	0.38	8	1416	13	3	10	0	21
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	0	0	0	0	4
4ENC_A	crcB links to Rfam database...	0.73	0.60	0.90	9	486	1	1	0	0	6
4FRG_B	AdoCbl-variant links to Rfam database...	0.60	0.58	0.64	14	1180	8	3	5	0	10
4FRN_A	AdoCbl-variant links to Rfam database...	0.19	0.18	0.22	5	1825	18	6	12	0	23
4JF2_A	preQ1-II links to Rfam database...	0.89	0.79	1.00	19	1063	0	0	0	0	5
4JRC_A	-	0.97	0.94	1.00	16	606	0	0	0	0	1

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