CompaRNA - on-line benchmarks of RNA structure prediction methods

FAQ

Metric	MaxExpect		PPfold(seed)
MCC	0.566	>	0.202
Average MCC ± 95% Confidence Intervals	0.539 ± 0.159	>	0.099 ± 0.109
Sensitivity	0.565	>	0.066
Positive Predictive Value	0.578	<	0.634
Total TP	222	>	26
Total TN	32327	<	32670
Total FP	220	>	80
Total FP CONTRA	54	>	1
Total FP INCONS	108	>	14
Total FP COMP	58	<	65
Total FN	171	<	367
P-value	2.97012568641e-08

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

Total Scores
MCC	0.566
Average MCC ± 95% Confidence Intervals	0.539 ± 0.159
Sensitivity	0.565
Positive Predictive Value	0.578
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...	-0.03	0.00	0.00	0	513	15	3	12	0	18
3J20_0	tRNA links to Rfam database...	0.53	0.57	0.50	12	1195	13	2	10	1	9
3J3D_C	tRNA links to Rfam database...	0.47	0.53	0.43	10	945	13	5	8	0	9
3J3E_8	5_8S_rRNA links to Rfam database...	0.10	0.13	0.09	2	2719	32	5	16	11	13
3J3F_8	5_8S_rRNA links to Rfam database...	0.34	0.42	0.29	8	4733	39	10	10	19	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...	0.70	0.69	0.71	20	1505	8	3	5	0	9
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...	0.97	0.94	1.00	31	1958	1	0	0	1	2
3ZEX_C	5_8S_rRNA links to Rfam database...	0.54	0.45	0.65	13	5354	17	2	5	10	16
4A1C_2	5_8S_rRNA links to Rfam database...	0.19	0.25	0.16	5	4484	41	10	17	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...	0.85	0.73	1.00	11	461	0	0	0	0	4
4ENC_A	crcB links to Rfam database...	0.36	0.33	0.42	5	484	8	0	7	1	10
4FRG_B	AdoCbl-variant links to Rfam database...	0.29	0.25	0.35	6	1185	11	4	7	0	18
4FRN_A	AdoCbl-variant links to Rfam database...	0.51	0.46	0.57	13	1825	10	5	5	0	15
4JF2_A	preQ1-II links to Rfam database...	0.89	0.79	1.00	19	1063	0	0	0	0	5

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.