CompaRNA - on-line benchmarks of RNA structure prediction methods

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Metric	RNASLOpt		Carnac(seed)
MCC	0.472	>	0.217
Average MCC ± 95% Confidence Intervals	0.489 ± 0.158	>	0.088 ± 0.134
Sensitivity	0.392	>	0.047
Positive Predictive Value	0.574	<	1.000
Total TP	190	>	23
Total TN	81473	<	81781
Total FP	184	>	0
Total FP CONTRA	21	>	0
Total FP INCONS	120	>	0
Total FP COMP	43	>	0
Total FN	295	<	462
P-value	1.77512146924e-08

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

Total Scores
MCC	0.472
Average MCC ± 95% Confidence Intervals	0.489 ± 0.158
Sensitivity	0.392
Positive Predictive Value	0.574
Nr of predictions	14

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...	0.47	0.35	0.64	7	1529	4	0	4	0	13
3J3E_8	5_8S_rRNA links to Rfam database...	0.00	0.00	0.00	0	7483	30	1	19	10	33
3J3F_8	5_8S_rRNA links to Rfam database...	0.34	0.33	0.35	12	12212	35	3	19	13	24
3W1K_J	tRNA-Sec links to Rfam database...	0.84	0.74	0.97	28	4157	1	1	0	0	10
3W3S_B	tRNA-Sec links to Rfam database...	0.82	0.70	0.97	28	4724	2	0	1	1	12
3ZEX_C	5_8S_rRNA links to Rfam database...	0.26	0.21	0.33	11	14163	35	2	20	13	41
4A1C_2	5_8S_rRNA links to Rfam database...	0.23	0.24	0.22	8	11744	35	8	21	6	25
4A1C_3	5S_rRNA links to Rfam database...	0.67	0.52	0.88	28	7108	4	0	4	0	26
4AOB_A	SAM links to Rfam database...	0.26	0.19	0.38	8	4350	13	2	11	0	34
4ENB_A	crcB links to Rfam database...	0.76	0.58	1.00	11	1264	0	0	0	0	8
4ENC_A	crcB links to Rfam database...	0.65	0.47	0.90	9	1316	1	1	0	0	10
4FRG_B	AdoCbl-variant links to Rfam database...	0.56	0.47	0.68	15	3464	7	1	6	0	17
4FRN_A	AdoCbl-variant links to Rfam database...	0.20	0.17	0.26	6	5128	17	2	15	0	30
4JF2_A	preQ1-II links to Rfam database...	0.78	0.61	1.00	19	2831	0	0	0	0	12

Total Scores
MCC	0.217
Average MCC ± 95% Confidence Intervals	0.088 ± 0.134
Sensitivity	0.047
Positive Predictive Value	1.000
Nr of predictions	14

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...	0.44	0.20	1.00	4	1536	0	0	0	0	16
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...	0.00	0.00	0.00	0	12246	0	0	0	0	36
3W1K_J	tRNA-Sec links to Rfam database...	0.00	0.00	0.00	0	4186	0	0	0	0	38
3W3S_B	tRNA-Sec links to Rfam database...	0.00	0.00	0.00	0	4753	0	0	0	0	40
3ZEX_C	5_8S_rRNA links to Rfam database...	0.00	0.00	0.00	0	14196	0	0	0	0	52
4A1C_2	5_8S_rRNA links to Rfam database...	0.00	0.00	0.00	0	11781	0	0	0	0	33
4A1C_3	5S_rRNA links to Rfam database...	0.00	0.00	0.00	0	7140	0	0	0	0	54
4AOB_A	SAM links to Rfam database...	0.00	0.00	0.00	0	4371	0	0	0	0	42
4ENB_A	crcB links to Rfam database...	0.00	0.00	0.00	0	1275	0	0	0	0	19
4ENC_A	crcB links to Rfam database...	0.00	0.00	0.00	0	1326	0	0	0	0	19
4FRG_B	AdoCbl-variant links to Rfam database...	0.00	0.00	0.00	0	3486	0	0	0	0	32
4FRN_A	AdoCbl-variant links to Rfam database...	0.00	0.00	0.00	0	5151	0	0	0	0	36
4JF2_A	preQ1-II links to Rfam database...	0.78	0.61	1.00	19	2831	0	0	0	0	12

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