CompaRNA - on-line benchmarks of RNA structure prediction methods

FAQ

Metric	HotKnots		PPfold(seed)
MCC	0.555	>	0.202
Average MCC ± 95% Confidence Intervals	0.579 ± 0.163	>	0.099 ± 0.109
Sensitivity	0.595	>	0.066
Positive Predictive Value	0.527	<	0.634
Total TP	234	>	26
Total TN	32267	<	32670
Total FP	258	>	80
Total FP CONTRA	69	>	1
Total FP INCONS	141	>	14
Total FP COMP	48	<	65
Total FN	159	<	367
P-value	3.10499527239e-08

Comparison of performance of HotKnots and PPfold(seed). 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 HotKnots and PPfold(seed)).
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 HotKnots and PPfold(seed)).
Comparison of average Matthews Correlation Coefficients (MCCs) for HotKnots and PPfold(seed). 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 HotKnots and PPfold(seed)).

Total Scores
MCC	0.555
Average MCC ± 95% Confidence Intervals	0.579 ± 0.163
Sensitivity	0.595
Positive Predictive Value	0.527
Nr of predictions	17

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...	0.64	0.61	0.69	11	512	5	0	5	0	7
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...	0.33	0.37	0.32	7	946	15	3	12	0	12
3J3E_8	5_8S_rRNA links to Rfam database...	0.15	0.20	0.12	3	2717	33	7	15	11	12
3J3F_8	5_8S_rRNA links to Rfam database...	0.33	0.42	0.26	8	4730	43	11	12	20	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...	0.77	0.76	0.79	22	1505	6	4	2	0	7
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...	0.60	0.61	0.61	20	1956	14	4	9	1	13
3ZEX_C	5_8S_rRNA links to Rfam database...	-0.01	0.00	0.00	0	5328	46	11	35	0	29
4A1C_2	5_8S_rRNA links to Rfam database...	0.19	0.25	0.15	5	4483	42	12	16	14	15
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...	1.00	1.00	1.00	15	457	0	0	0	0	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...	0.36	0.38	0.38	9	1178	15	2	13	0	15
4FRN_A	AdoCbl-variant links to Rfam database...	0.59	0.57	0.62	16	1822	10	2	8	0	12
4JF2_A	preQ1-II links to Rfam database...	0.92	1.00	0.86	24	1054	4	4	0	0	0

Total Scores
MCC	0.202
Average MCC ± 95% Confidence Intervals	0.099 ± 0.109
Sensitivity	0.066
Positive Predictive Value	0.634
Nr of predictions	17

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...	0.49	0.33	0.75	6	520	2	0	2	0	12
3J20_0	tRNA links to Rfam database...	0.00	0.00	0.00	0	1219	0	0	0	0	21
3J3D_C	tRNA links to Rfam database...	0.00	0.00	0.00	0	968	0	0	0	0	19
3J3E_8	5_8S_rRNA links to Rfam database...	0.00	0.00	0.00	0	2742	6	0	0	6	15
3J3F_8	5_8S_rRNA links to Rfam database...	0.19	0.11	0.33	2	4755	24	0	4	20	17
3RKF_A	Purine links to Rfam database...	0.00	0.00	0.00	0	866	0	0	0	0	24
3SD1_A	THF links to Rfam database...	0.00	0.00	0.00	0	1533	0	0	0	0	29
3W1K_J	tRNA-Sec links to Rfam database...	0.00	0.00	0.00	0	1678	0	0	0	0	31
3W3S_B	tRNA-Sec links to Rfam database...	0.00	0.00	0.00	0	1989	0	0	0	0	33
3ZEX_C	5_8S_rRNA links to Rfam database...	0.15	0.07	0.33	2	5368	24	0	4	20	27
4A1C_2	5_8S_rRNA links to Rfam database...	0.10	0.05	0.20	1	4511	23	0	4	19	19
4AOB_A	SAM links to Rfam database...	0.00	0.00	0.00	0	1437	0	0	0	0	29
4ENB_A	crcB links to Rfam database...	0.00	0.00	0.00	0	472	0	0	0	0	15
4ENC_A	crcB links to Rfam database...	0.00	0.00	0.00	0	496	0	0	0	0	15
4FRG_B	AdoCbl-variant links to Rfam database...	0.00	0.00	0.00	0	1202	0	0	0	0	24
4FRN_A	AdoCbl-variant links to Rfam database...	0.00	0.00	0.00	0	1848	0	0	0	0	28
4JF2_A	preQ1-II links to Rfam database...	0.76	0.63	0.94	15	1066	1	1	0	0	9

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