CompaRNA - on-line benchmarks of RNA structure prediction methods

FAQ

Metric	RNAalifold(seed)		ProbKnot
MCC	0.602	>	0.495
Average MCC ± 95% Confidence Intervals	0.503 ± 0.103	<	0.509 ± 0.122
Sensitivity	0.425	<	0.442
Positive Predictive Value	0.854	>	0.556
Total TP	653	<	680
Total TN	1361558	>	1361099
Total FP	126	<	615
Total FP CONTRA	15	<	77
Total FP INCONS	97	<	467
Total FP COMP	14	<	71
Total FN	884	>	857
P-value	5.10776592382e-08

Comparison of performance of RNAalifold(seed) and ProbKnot. 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 RNAalifold(seed) and ProbKnot).
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 RNAalifold(seed) and ProbKnot).
Comparison of average Matthews Correlation Coefficients (MCCs) for RNAalifold(seed) and ProbKnot. 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 RNAalifold(seed) and ProbKnot).

Total Scores
MCC	0.602
Average MCC ± 95% Confidence Intervals	0.503 ± 0.103
Sensitivity	0.425
Positive Predictive Value	0.854
Nr of predictions	22

RNA Chain	Rfam family	MCC	SENS	PPV	TP	TN	FP	FP CONTRA	FP INCONS	FP COMP	FN
2KX8_A	7SK links to Rfam database...	0.00	0.00	0.00	0	861	0	0	0	0	18
2LC8_A	GP_knot1 links to Rfam database...	-0.01	0.00	0.00	0	1528	12	0	12	0	20
3IYQ_A	tmRNA links to Rfam database...	0.38	0.21	0.69	20	60697	13	5	4	4	74
3IZ4_A	tmRNA links to Rfam database...	0.42	0.21	0.85	28	70843	5	1	4	0	104
3J20_2	SSU_rRNA_archaea links to Rfam database...	0.69	0.58	0.83	367	1116322	80	5	71	4	266
3J3E_8	5_8S_rRNA links to Rfam database...	0.00	0.00	0.00	0	7503	0	0	0	0	33
3J3F_8	5_8S_rRNA links to Rfam database...	0.50	0.25	1.00	9	12237	0	0	0	0	27
3NPB_A	SAM links to Rfam database...	0.66	0.48	0.92	22	6997	3	1	1	1	24
3O58_3	5_8S_rRNA links to Rfam database...	0.51	0.26	1.00	9	12394	0	0	0	0	26
3PDR_A	ykoK links to Rfam database...	0.68	0.46	1.00	33	12847	1	0	0	1	39
3RKF_A	Purine links to Rfam database...	0.63	0.47	0.84	16	2192	3	1	2	0	18
3SD1_A	THF links to Rfam database...	0.58	0.40	0.85	17	3896	3	1	2	0	25
3W1K_J	tRNA-Sec links to Rfam database...	0.71	0.50	1.00	19	4167	0	0	0	0	19
3W3S_B	tRNA-Sec links to Rfam database...	0.67	0.45	1.00	18	4735	1	0	0	1	22
3ZEX_C	5_8S_rRNA links to Rfam database...	0.42	0.17	1.00	9	14187	0	0	0	0	43
4A1C_2	5_8S_rRNA links to Rfam database...	0.39	0.15	1.00	5	11776	2	0	0	2	28
4AOB_A	SAM links to Rfam database...	0.72	0.52	1.00	22	4349	1	0	0	1	20
4ENB_A	crcB links to Rfam database...	0.56	0.32	1.00	6	1269	0	0	0	0	13
4ENC_A	crcB links to Rfam database...	0.56	0.32	1.00	6	1320	0	0	0	0	13
4FRG_B	AdoCbl-variant links to Rfam database...	0.73	0.53	1.00	17	3469	0	0	0	0	15
4FRN_A	AdoCbl-variant links to Rfam database...	0.69	0.53	0.90	19	5130	2	1	1	0	17
4JF2_A	preQ1-II links to Rfam database...	0.59	0.35	1.00	11	2839	0	0	0	0	20

Total Scores
MCC	0.495
Average MCC ± 95% Confidence Intervals	0.509 ± 0.122
Sensitivity	0.442
Positive Predictive Value	0.556
Nr of predictions	22

RNA Chain	Rfam family	MCC	SENS	PPV	TP	TN	FP	FP CONTRA	FP INCONS	FP COMP	FN
2KX8_A	7SK links to Rfam database...	0.94	0.89	1.00	16	845	0	0	0	0	2
2LC8_A	GP_knot1 links to Rfam database...	-0.01	0.00	0.00	0	1525	15	2	13	0	20
3IYQ_A	tmRNA links to Rfam database...	0.28	0.31	0.26	29	60616	85	22	59	4	65
3IZ4_A	tmRNA links to Rfam database...	0.52	0.46	0.60	61	70774	46	6	35	5	71
3J20_2	SSU_rRNA_archaea links to Rfam database...	0.50	0.43	0.57	272	1116290	208	11	192	5	361
3J3E_8	5_8S_rRNA links to Rfam database...	0.00	0.00	0.00	0	7476	37	3	24	10	33
3J3F_8	5_8S_rRNA links to Rfam database...	0.35	0.33	0.36	12	12213	35	3	18	14	24
3NPB_A	SAM links to Rfam database...	0.72	0.61	0.85	28	6988	8	1	4	3	18
3O58_3	5_8S_rRNA links to Rfam database...	0.31	0.34	0.29	12	12362	41	4	25	12	23
3PDR_A	ykoK links to Rfam database...	0.74	0.64	0.85	46	12826	10	1	7	2	26
3RKF_A	Purine links to Rfam database...	0.73	0.59	0.91	20	2189	2	1	1	0	14
3SD1_A	THF links to Rfam database...	0.55	0.48	0.65	20	3885	11	2	9	0	22
3W1K_J	tRNA-Sec links to Rfam database...	0.87	0.79	0.97	30	4155	1	1	0	0	8
3W3S_B	tRNA-Sec links to Rfam database...	0.89	0.80	1.00	32	4721	1	0	0	1	8
3ZEX_C	5_8S_rRNA links to Rfam database...	0.38	0.31	0.47	16	14162	21	2	16	3	36
4A1C_2	5_8S_rRNA links to Rfam database...	0.13	0.15	0.12	5	11738	49	7	31	11	28
4AOB_A	SAM links to Rfam database...	0.50	0.40	0.63	17	4344	11	2	8	1	25
4ENB_A	crcB links to Rfam database...	0.73	0.58	0.92	11	1263	1	1	0	0	8
4ENC_A	crcB links to Rfam database...	0.45	0.42	0.50	8	1310	8	1	7	0	11
4FRG_B	AdoCbl-variant links to Rfam database...	0.37	0.31	0.45	10	3464	12	3	9	0	22
4FRN_A	AdoCbl-variant links to Rfam database...	0.44	0.36	0.54	13	5127	11	2	9	0	23
4JF2_A	preQ1-II links to Rfam database...	0.80	0.71	0.92	22	2826	2	2	0	0	9

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