CompaRNA - on-line benchmarks of RNA structure prediction methods

Laboratory of Structural Bioinformatics @ Adam Mickiewicz University in Poznan

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Overview

Metric	RNAshapes		MCFold
MCC	0.756	>	0.622
Average MCC ± 95% Confidence Intervals	0.768 ± 0.052	>	0.657 ± 0.062
Sensitivity	0.768	>	0.663
Positive Predictive Value	0.753	>	0.597
Total TP	1670	>	1441
Total TN	133989	>	133792
Total FP	864	<	1310
Total FP CONTRA	139	<	262
Total FP INCONS	409	<	712
Total FP COMP	316	<	336
Total FN	505	<	734
P-value	3.56938820447e-08

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Performance plots

Comparison of performance of RNAshapes and MCFold. 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 RNAshapes and MCFold).
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 RNAshapes and MCFold).
Comparison of average Matthews Correlation Coefficients (MCCs) for RNAshapes and MCFold. 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 RNAshapes and MCFold).

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Performance of RNAshapes - scored higher in this pairwise comparison

1. Total counts & total scores for RNAshapes

Total Base Pair Counts
Total TP	1670
Total TN	133989
Total FP	864
Total FP CONTRA	139
Total FP INCONS	409
Total FP COMP	316
Total FN	505

Total Scores
MCC	0.756
Average MCC ± 95% Confidence Intervals	0.768 ± 0.052
Sensitivity	0.768
Positive Predictive Value	0.753
Nr of predictions	131

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2. Individual counts for RNAshapes [ download as .csv ]

RNA Chain	Rfam family	MCC	SENS	PPV	TP	TN	FP	FP CONTRA	FP INCONS	FP COMP	FN
2K5Z_A	-	1.00	1.00	1.00	11	175	0	0	0	0	0
2K63_A	-	1.00	1.00	1.00	9	159	0	0	0	0	0
2K66_A	-	1.00	1.00	1.00	9	80	0	0	0	0	0
2KD8_A	-	1.00	1.00	1.00	9	99	0	0	0	0	0
2KDQ_B	mir-TAR links to Rfam database...	1.00	1.00	1.00	10	164	0	0	0	0	0
2KE6_A	K10_TLS links to Rfam database...	1.00	1.00	1.00	18	449	1	0	0	1	0
2KEZ_A	-	1.00	1.00	1.00	8	94	0	0	0	0	0
2KFC_A	-	-0.03	0.00	0.00	0	229	7	1	6	0	8
2KGP_A	-	1.00	1.00	1.00	9	112	1	0	0	1	0
2KMJ_A	-	1.00	1.00	1.00	11	157	0	0	0	0	0
2KPV_A	-	0.96	0.92	1.00	12	201	0	0	0	0	1
2KU0_A	-	0.96	0.92	1.00	11	281	0	0	0	0	1
2KUR_A	K10_TLS links to Rfam database...	1.00	1.00	1.00	19	448	0	0	0	0	0
2KUU_A	K10_TLS links to Rfam database...	1.00	1.00	1.00	18	429	1	0	0	1	0
2KUV_A	K10_TLS links to Rfam database...	1.00	1.00	1.00	19	420	0	0	0	0	0
2KUW_A	K10_TLS links to Rfam database...	1.00	1.00	1.00	18	452	1	0	0	1	0
2KX8_A	7SK links to Rfam database...	0.97	0.94	1.00	15	356	0	0	0	0	1
2KXM_A	-	0.93	0.88	1.00	7	142	0	0	0	0	1
2KZL_A	-	1.00	1.00	1.00	13	507	1	0	0	1	0
2L1F_A	Gammaretro_CES links to Rfam database...	0.89	0.87	0.91	20	741	2	0	2	0	3
2L1F_B	Gammaretro_CES links to Rfam database...	0.98	0.96	1.00	23	768	0	0	0	0	1
2L2K_A	-	0.97	0.94	1.00	16	333	0	0	0	0	1
2L3C_B	-	1.00	1.00	1.00	14	225	0	0	0	0	0
2L3E_A	-	1.00	1.00	1.00	12	228	1	0	0	1	0
2L3J_B	mir-2985-2 links to Rfam database...	0.98	0.97	1.00	29	956	0	0	0	0	1
2L5Z_A	-	1.00	1.00	1.00	9	102	0	0	0	0	0
2L94_A	HIV_FE links to Rfam database...	1.00	1.00	1.00	18	339	1	0	0	1	0
2LA5_A	-	0.77	0.71	0.83	5	269	3	0	1	2	2
2LBS_A	-	1.00	1.00	1.00	14	193	0	0	0	0	0
2LC8_A	GP_knot1 links to Rfam database...	0.64	0.61	0.69	11	512	5	0	5	0	7
2LDL_A	-	1.00	1.00	1.00	9	131	1	0	0	1	0
2LDT_A	-	1.00	1.00	1.00	11	151	0	0	0	0	0
2LHP_A	-	1.00	1.00	1.00	15	246	0	0	0	0	0
2LI4_A	-	1.00	1.00	1.00	14	175	0	0	0	0	0
2LJJ_A	-	1.00	1.00	1.00	7	123	3	0	0	3	0
2LK3_A	-	1.00	1.00	1.00	9	91	0	0	0	0	0
2LKR_A	-	1.00	1.00	1.00	29	2411	6	0	0	6	0
2LQZ_A	-	1.00	1.00	1.00	8	124	2	0	0	2	0
2LU0_A	-	1.00	1.00	1.00	16	422	0	0	0	0	0
2LWK_A	-	0.95	0.91	1.00	10	197	1	0	0	1	1
2M58_A	-	0.40	0.42	0.42	5	532	7	1	6	0	7
2RP0_A	-	0.84	0.71	1.00	5	111	0	0	0	0	2
2RPT_A	-	1.00	1.00	1.00	7	65	0	0	0	0	0
2RRC_A	-	0.83	0.71	1.00	5	70	0	0	0	0	2
2WRQ_Y	tRNA links to Rfam database...	1.00	1.00	1.00	9	1143	13	0	0	13	0
2WW9_F	-	0.68	0.75	0.67	6	103	4	1	2	1	2
2WW9_D	-	0.11	0.10	0.14	1	734	11	2	4	5	9
2WW9_E	-	0.89	0.80	1.00	4	168	0	0	0	0	1
2WWQ_V	tRNA links to Rfam database...	1.00	1.00	1.00	19	1185	5	0	0	5	0
2XKV_B	Bacteria_small_SRP links to Rfam database...	0.64	0.73	0.57	8	1821	24	0	6	18	3
2XQD_Y	tRNA links to Rfam database...	0.70	0.67	0.74	14	1110	6	0	5	1	7
2XXA_G	Bacteria_small_SRP links to Rfam database...	1.00	1.00	1.00	35	2010	1	0	0	1	0
2Y8W_B	-	1.00	1.00	1.00	6	82	1	0	0	1	0
2Y9C_V	-	0.79	0.83	0.75	15	886	8	0	5	3	3
2YIE_Z	-	-0.02	0.00	0.00	0	587	15	6	9	0	8
2YIE_X	-	0.33	0.43	0.27	3	533	11	3	5	3	4
2ZY6_A	-	0.69	0.78	0.64	7	265	5	2	2	1	2
2ZZN_D	tRNA links to Rfam database...	0.77	0.77	0.77	17	962	5	1	4	0	5
3A2K_C	tRNA links to Rfam database...	0.47	0.50	0.46	11	1084	13	3	10	0	11
3A3A_A	tRNA-Sec links to Rfam database...	0.84	0.80	0.89	24	1473	3	0	3	0	6
3AKZ_H	tRNA links to Rfam database...	0.78	0.80	0.76	16	1106	7	2	3	2	4
3AM1_B	-	0.71	0.72	0.70	21	1436	9	3	6	0	8
3AMU_B	tRNA links to Rfam database...	0.81	0.79	0.83	15	1139	6	0	3	3	4
3DW4_A	-	-0.03	0.00	0.00	0	137	3	0	3	0	6
3GCA_A	-	0.84	0.71	1.00	5	153	0	0	0	0	2
3GX2_A	SAM links to Rfam database...	0.91	0.89	0.93	25	1422	3	1	1	1	3
3HAY_E	-	1.00	1.00	1.00	14	910	5	0	0	5	0
3HJW_D	-	1.00	1.00	1.00	16	593	0	0	0	0	0
3IAB_R	-	1.00	1.00	1.00	12	373	0	0	0	0	0
3ID5_D	-	0.59	0.60	0.60	3	224	5	0	2	3	2
3IVN_B	Purine links to Rfam database...	0.91	0.83	1.00	19	884	0	0	0	0	4
3IWN_A	c-di-GMP-I links to Rfam database...	0.83	0.79	0.88	22	1447	3	1	2	0	6
3IZF_C	5S_rRNA links to Rfam database...	0.76	0.77	0.75	27	2604	14	0	9	5	8
3J0L_8	-	1.00	1.00	1.00	7	69	0	0	0	0	0
3J0L_2	-	0.46	0.46	0.48	12	2225	20	1	12	7	14
3J0L_g	-	-0.01	0.00	0.00	0	174	4	0	2	2	2
3J0L_7	-	-0.02	0.00	0.00	0	507	12	2	10	0	10
3J0L_h	-	0.87	0.81	0.93	26	2112	4	1	1	2	6
3J0L_1	-	0.83	0.77	0.91	10	473	4	0	1	3	3
3J0L_a	-	0.18	0.18	0.22	2	402	8	3	4	1	9
3J16_L	tRNA links to Rfam database...	0.59	0.57	0.63	12	1140	7	0	7	0	9
3J20_0	tRNA links to Rfam database...	0.51	0.57	0.48	12	1194	14	3	10	1	9
3J2L_3	5S_rRNA links to Rfam database...	0.77	0.79	0.75	27	2984	14	1	8	5	7
3J3D_C	tRNA links to Rfam database...	0.63	0.68	0.59	13	946	9	3	6	0	6
3J3E_8	5_8S_rRNA links to Rfam database...	0.26	0.33	0.21	5	2718	29	6	13	10	10
3J3E_7	5S_rRNA links to Rfam database...	0.64	0.65	0.65	22	2707	16	1	11	4	12
3J3F_7	5S_rRNA links to Rfam database...	0.83	0.81	0.85	29	2900	7	0	5	2	7
3J3F_8	5_8S_rRNA links to Rfam database...	0.33	0.42	0.26	8	4730	42	11	12	19	11
3JYV_7	tRNA links to Rfam database...	-0.02	0.00	0.00	0	1092	20	1	18	1	20
3JYX_3	5S_rRNA links to Rfam database...	0.77	0.80	0.75	12	2362	26	0	4	22	3
3JYX_4	5_8S_rRNA links to Rfam database...	0.61	0.83	0.45	10	4734	35	10	2	23	2
3KTW_C	-	0.57	0.60	0.56	15	1753	19	2	10	7	10
3LA5_A	Purine links to Rfam database...	0.89	0.80	1.00	20	934	0	0	0	0	5
3NDB_M	-	0.98	0.98	0.98	43	3670	5	0	1	4	1
3NKB_B	-	0.75	0.74	0.78	14	717	6	0	4	2	5
3NMU_E	-	1.00	1.00	1.00	3	213	5	0	0	5	0
3O58_3	5_8S_rRNA links to Rfam database...	0.41	0.50	0.34	11	4732	38	6	15	17	11
3O58_2	5S_rRNA links to Rfam database...	0.73	0.74	0.72	23	2722	18	0	9	9	8
3OVB_D	-	1.00	1.00	1.00	11	215	1	0	0	1	0
3OVS_D	-	1.00	1.00	1.00	12	204	0	0	0	0	0
3P22_G	-	1.00	1.00	1.00	11	301	0	0	0	0	0
3PDR_A	ykoK links to Rfam database...	0.80	0.80	0.80	40	4790	12	3	7	2	10
3R4F_A	-	1.00	1.00	1.00	22	884	1	0	0	1	0
3R9X_C	-	1.00	1.00	1.00	8	221	2	0	0	2	0
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
3SIU_F	-	1.00	1.00	1.00	8	137	0	0	0	0	0
3SN2_B	IRE_II links to Rfam database...	0.95	0.92	1.00	11	143	0	0	0	0	1
3TRZ_Z	-	1.00	1.00	1.00	5	87	1	0	0	1	0
3TS0_U	-	1.00	1.00	1.00	6	112	1	0	0	1	0
3TS2_V	-	1.00	1.00	1.00	5	103	0	0	0	0	0
3U4M_B	-	0.49	0.55	0.46	12	1250	14	3	11	0	10
3VJR_D	-	1.00	1.00	1.00	12	239	0	0	0	0	0
3ZEX_G	-	0.66	0.67	0.67	30	6462	27	4	11	12	15
3ZEX_F	-	-0.01	0.00	0.00	0	908	11	2	4	5	4
3ZEX_C	5_8S_rRNA links to Rfam database...	0.29	0.34	0.26	10	5335	42	5	24	13	19
3ZEX_H	-	0.28	0.37	0.22	7	3593	32	11	14	7	12
3ZEX_D	5S_rRNA links to Rfam database...	0.86	0.80	0.93	28	2766	6	0	2	4	7
3ZND_W	tRNA links to Rfam database...	0.24	0.38	0.16	3	1172	24	9	7	8	5
4A1C_2	5_8S_rRNA links to Rfam database...	0.19	0.25	0.16	5	4484	41	11	16	14	15
4A1C_3	5S_rRNA links to Rfam database...	0.86	0.84	0.89	31	2728	7	0	4	3	6
4A4U_A	-	1.00	1.00	1.00	9	96	0	0	0	0	0
4ATO_G	-	0.38	0.43	0.38	3	212	5	5	0	0	4
4ENB_A	crcB links to Rfam database...	0.85	0.73	1.00	11	461	2	0	0	2	4
4ENC_A	crcB links to Rfam database...	0.37	0.33	0.45	5	485	7	0	6	1	10
4FNJ_A	-	0.91	0.83	1.00	10	240	0	0	0	0	2
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
4HXH_A	-	1.00	1.00	1.00	6	89	0	0	0	0	0
4JF2_A	preQ1-II links to Rfam database...	0.89	0.79	1.00	19	1063	0	0	0	0	5
4JRC_A	-	0.34	0.35	0.35	6	605	11	0	11	0	11

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Performance of MCFold - scored lower in this pairwise comparison

1. Total counts & total scores for MCFold

Total Base Pair Counts
Total TP	1441
Total TN	133792
Total FP	1310
Total FP CONTRA	262
Total FP INCONS	712
Total FP COMP	336
Total FN	734

Total Scores
MCC	0.622
Average MCC ± 95% Confidence Intervals	0.657 ± 0.062
Sensitivity	0.663
Positive Predictive Value	0.597
Nr of predictions	131

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2. Individual counts for MCFold [ download as .csv ]

RNA Chain	Rfam family	MCC	SENS	PPV	TP	TN	FP	FP CONTRA	FP INCONS	FP COMP	FN
2K5Z_A	-	1.00	1.00	1.00	11	175	0	0	0	0	0
2K63_A	-	1.00	1.00	1.00	9	159	4	0	0	4	0
2K66_A	-	1.00	1.00	1.00	9	80	0	0	0	0	0
2KD8_A	-	1.00	1.00	1.00	9	99	1	0	0	1	0
2KDQ_B	mir-TAR links to Rfam database...	1.00	1.00	1.00	10	164	1	0	0	1	0
2KE6_A	K10_TLS links to Rfam database...	1.00	1.00	1.00	18	449	1	0	0	1	0
2KEZ_A	-	1.00	1.00	1.00	8	94	0	0	0	0	0
2KFC_A	-	0.54	0.63	0.50	5	226	5	2	3	0	3
2KGP_A	-	1.00	1.00	1.00	9	112	1	0	0	1	0
2KMJ_A	-	1.00	1.00	1.00	11	157	1	0	0	1	0
2KPV_A	-	1.00	1.00	1.00	13	200	0	0	0	0	0
2KU0_A	-	1.00	1.00	1.00	12	280	1	0	0	1	0
2KUR_A	K10_TLS links to Rfam database...	1.00	1.00	1.00	19	448	0	0	0	0	0
2KUU_A	K10_TLS links to Rfam database...	1.00	1.00	1.00	18	429	1	0	0	1	0
2KUV_A	K10_TLS links to Rfam database...	1.00	1.00	1.00	19	420	0	0	0	0	0
2KUW_A	K10_TLS links to Rfam database...	1.00	1.00	1.00	18	452	1	0	0	1	0
2KX8_A	7SK links to Rfam database...	1.00	1.00	1.00	16	355	0	0	0	0	0
2KXM_A	-	1.00	1.00	1.00	8	141	1	0	0	1	0
2KZL_A	-	1.00	1.00	1.00	13	507	5	0	0	5	0
2L1F_A	Gammaretro_CES links to Rfam database...	0.79	0.78	0.82	18	741	4	0	4	0	5
2L1F_B	Gammaretro_CES links to Rfam database...	0.80	0.79	0.83	19	768	4	0	4	0	5
2L2K_A	-	1.00	1.00	1.00	17	332	1	0	0	1	0
2L3C_B	-	1.00	1.00	1.00	14	225	1	0	0	1	0
2L3E_A	-	1.00	1.00	1.00	12	228	2	0	0	2	0
2L3J_B	mir-2985-2 links to Rfam database...	1.00	1.00	1.00	30	955	0	0	0	0	0
2L5Z_A	-	1.00	1.00	1.00	9	102	0	0	0	0	0
2L94_A	HIV_FE links to Rfam database...	1.00	1.00	1.00	18	339	1	0	0	1	0
2LA5_A	-	-0.03	0.00	0.00	0	265	10	0	10	0	7
2LBS_A	-	1.00	1.00	1.00	14	193	1	0	0	1	0
2LC8_A	GP_knot1 links to Rfam database...	0.44	0.44	0.47	8	511	10	0	9	1	10
2LDL_A	-	1.00	1.00	1.00	9	131	1	0	0	1	0
2LDT_A	-	0.95	0.91	1.00	10	152	0	0	0	0	1
2LHP_A	-	1.00	1.00	1.00	15	246	1	0	0	1	0
2LI4_A	-	1.00	1.00	1.00	14	175	0	0	0	0	0
2LJJ_A	-	1.00	1.00	1.00	7	123	3	0	0	3	0
2LK3_A	-	1.00	1.00	1.00	9	91	0	0	0	0	0
2LKR_A	-	1.00	1.00	1.00	29	2411	11	0	0	11	0
2LQZ_A	-	1.00	1.00	1.00	8	124	3	0	0	3	0
2LU0_A	-	1.00	1.00	1.00	16	422	2	0	0	2	0
2LWK_A	-	1.00	1.00	1.00	11	196	2	0	0	2	0
2M58_A	-	0.22	0.25	0.23	3	531	13	1	9	3	9
2RP0_A	-	0.70	0.71	0.71	5	109	2	1	1	0	2
2RPT_A	-	1.00	1.00	1.00	7	65	0	0	0	0	0
2RRC_A	-	1.00	1.00	1.00	7	68	1	0	0	1	0
2WRQ_Y	tRNA links to Rfam database...	0.38	0.56	0.26	5	1133	21	8	6	7	4
2WW9_F	-	0.68	0.75	0.67	6	103	4	1	2	1	2
2WW9_D	-	-0.02	0.00	0.00	0	723	21	6	12	3	10
2WW9_E	-	-0.03	0.00	0.00	0	165	8	1	6	1	5
2WWQ_V	tRNA links to Rfam database...	0.19	0.21	0.19	4	1183	20	3	14	3	15
2XKV_B	Bacteria_small_SRP links to Rfam database...	0.20	0.27	0.16	3	1816	30	4	12	14	8
2XQD_Y	tRNA links to Rfam database...	0.39	0.43	0.38	9	1105	18	2	13	3	12
2XXA_G	Bacteria_small_SRP links to Rfam database...	0.23	0.26	0.24	9	2007	30	1	28	1	26
2Y8W_B	-	1.00	1.00	1.00	6	82	2	0	0	2	0
2Y9C_V	-	0.65	0.72	0.59	13	884	12	1	8	3	5
2YIE_Z	-	0.53	0.63	0.45	5	591	8	2	4	2	3
2YIE_X	-	-0.01	0.00	0.00	0	535	15	1	8	6	7
2ZY6_A	-	0.77	0.78	0.78	7	267	6	1	1	4	2
2ZZN_D	tRNA links to Rfam database...	0.69	0.73	0.67	16	960	11	1	7	3	6
3A2K_C	tRNA links to Rfam database...	0.49	0.55	0.46	12	1082	14	3	11	0	10
3A3A_A	tRNA-Sec links to Rfam database...	0.98	0.97	1.00	29	1471	0	0	0	0	1
3AKZ_H	tRNA links to Rfam database...	0.46	0.50	0.43	10	1104	16	5	8	3	10
3AM1_B	-	1.00	1.00	1.00	29	1437	1	0	0	1	0
3AMU_B	tRNA links to Rfam database...	0.50	0.58	0.44	11	1132	15	4	10	1	8
3DW4_A	-	1.00	1.00	1.00	6	134	3	0	0	3	0
3GCA_A	-	-0.05	0.00	0.00	0	150	8	4	4	0	7
3GX2_A	SAM links to Rfam database...	0.58	0.61	0.57	17	1419	15	1	12	2	11
3HAY_E	-	1.00	1.00	1.00	14	910	10	0	0	10	0
3HJW_D	-	1.00	1.00	1.00	16	593	5	0	0	5	0
3IAB_R	-	1.00	1.00	1.00	12	373	4	0	0	4	0
3ID5_D	-	0.54	0.60	0.50	3	223	7	1	2	4	2
3IVN_B	Purine links to Rfam database...	0.45	0.48	0.46	11	879	14	5	8	1	12
3IWN_A	c-di-GMP-I links to Rfam database...	0.19	0.21	0.20	6	1442	24	5	19	0	22
3IZF_C	5S_rRNA links to Rfam database...	0.92	0.94	0.89	33	2603	10	0	4	6	2
3J0L_8	-	1.00	1.00	1.00	7	69	0	0	0	0	0
3J0L_2	-	0.25	0.27	0.25	7	2222	29	4	17	8	19
3J0L_g	-	-0.02	0.00	0.00	0	170	7	4	2	1	2
3J0L_7	-	-0.02	0.00	0.00	0	504	15	6	9	0	10
3J0L_h	-	0.98	0.97	1.00	31	2109	2	0	0	2	1
3J0L_1	-	0.88	0.85	0.92	11	472	5	0	1	4	2
3J0L_a	-	0.14	0.18	0.15	2	398	13	1	10	2	9
3J16_L	tRNA links to Rfam database...	0.54	0.57	0.52	12	1136	12	4	7	1	9
3J20_0	tRNA links to Rfam database...	0.66	0.71	0.63	15	1195	11	3	6	2	6
3J2L_3	5S_rRNA links to Rfam database...	0.77	0.79	0.75	27	2984	15	1	8	6	7
3J3D_C	tRNA links to Rfam database...	0.54	0.63	0.48	12	943	13	4	9	0	7
3J3E_8	5_8S_rRNA links to Rfam database...	0.15	0.20	0.12	3	2716	36	11	12	13	12
3J3E_7	5S_rRNA links to Rfam database...	0.55	0.56	0.54	19	2706	23	1	15	7	15
3J3F_7	5S_rRNA links to Rfam database...	0.88	0.89	0.86	32	2897	9	1	4	4	4
3J3F_8	5_8S_rRNA links to Rfam database...	0.14	0.21	0.10	4	4720	51	17	20	14	15
3JYV_7	tRNA links to Rfam database...	0.25	0.30	0.24	6	1086	20	8	11	1	14
3JYX_3	5S_rRNA links to Rfam database...	0.46	0.67	0.32	10	2347	28	15	6	7	5
3JYX_4	5_8S_rRNA links to Rfam database...	0.36	0.58	0.23	7	4725	37	19	5	13	5
3KTW_C	-	0.55	0.60	0.52	15	1751	20	4	10	6	10
3LA5_A	Purine links to Rfam database...	0.44	0.44	0.48	11	931	12	2	10	0	14
3NDB_M	-	0.29	0.30	0.30	13	3671	35	1	29	5	31
3NKB_B	-	0.68	0.74	0.64	14	713	8	2	6	0	5
3NMU_E	-	0.51	0.67	0.40	2	211	8	1	2	5	1
3O58_3	5_8S_rRNA links to Rfam database...	0.28	0.36	0.22	8	4727	39	14	15	10	14
3O58_2	5S_rRNA links to Rfam database...	0.25	0.29	0.23	9	2715	31	6	24	1	22
3OVB_D	-	1.00	1.00	1.00	11	215	1	0	0	1	0
3OVS_D	-	1.00	1.00	1.00	12	204	0	0	0	0	0
3P22_G	-	1.00	1.00	1.00	11	301	1	0	0	1	0
3PDR_A	ykoK links to Rfam database...	0.78	0.80	0.77	40	4788	14	5	7	2	10
3R4F_A	-	0.95	0.95	0.95	21	884	4	0	1	3	1
3R9X_C	-	0.87	0.88	0.88	7	221	5	0	1	4	1
3RKF_A	Purine links to Rfam database...	0.89	0.88	0.91	21	843	3	0	2	1	3
3SD1_A	THF links to Rfam database...	0.43	0.45	0.43	13	1503	17	1	16	0	16
3SIU_F	-	0.53	0.63	0.50	5	135	5	2	3	0	3
3SN2_B	IRE_II links to Rfam database...	0.58	0.58	0.64	7	143	4	0	4	0	5
3TRZ_Z	-	-0.05	0.00	0.00	0	88	4	0	4	0	5
3TS0_U	-	1.00	1.00	1.00	6	112	1	0	0	1	0
3TS2_V	-	-0.05	0.00	0.00	0	102	7	0	6	1	5
3U4M_B	-	0.74	0.77	0.71	17	1252	10	1	6	3	5
3VJR_D	-	1.00	1.00	1.00	12	239	1	0	0	1	0
3ZEX_G	-	0.00	0.00	0.00	0	6493	14	6	8	0	45
3ZEX_F	-	0.00	0.00	0.00	0	909	22	0	5	17	4
3ZEX_C	5_8S_rRNA links to Rfam database...	0.30	0.34	0.27	10	5337	28	6	21	1	19
3ZEX_H	-	0.22	0.32	0.16	6	3588	36	15	16	5	13
3ZEX_D	5S_rRNA links to Rfam database...	0.23	0.26	0.23	9	2756	33	6	25	2	26
3ZND_W	tRNA links to Rfam database...	0.23	0.38	0.15	3	1171	26	9	8	9	5
4A1C_2	5_8S_rRNA links to Rfam database...	0.18	0.25	0.14	5	4480	45	12	19	14	15
4A1C_3	5S_rRNA links to Rfam database...	0.86	0.86	0.86	32	2726	9	0	5	4	5
4A4U_A	-	1.00	1.00	1.00	9	96	0	0	0	0	0
4ATO_G	-	0.36	0.43	0.33	3	211	8	0	6	2	4
4ENB_A	crcB links to Rfam database...	0.78	0.73	0.85	11	459	4	0	2	2	4
4ENC_A	crcB links to Rfam database...	0.34	0.33	0.38	5	483	11	0	8	3	10
4FNJ_A	-	0.91	0.92	0.92	11	238	1	0	1	0	1
4FRG_B	AdoCbl-variant links to Rfam database...	0.35	0.38	0.35	9	1176	17	3	14	0	15
4FRN_A	AdoCbl-variant links to Rfam database...	0.09	0.11	0.10	3	1818	28	2	25	1	25
4HXH_A	-	1.00	1.00	1.00	6	89	0	0	0	0	0
4JF2_A	preQ1-II links to Rfam database...	0.74	0.75	0.75	18	1058	7	1	5	1	6
4JRC_A	-	0.24	0.29	0.23	5	600	17	0	17	0	12

^top

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

Table of contents:

Overview

Performance plots

Performance of RNAshapes - scored higher in this pairwise comparison

1. Total counts & total scores for RNAshapes

2. Individual counts for RNAshapes [ download as .csv ]

Performance of MCFold - scored lower in this pairwise comparison

1. Total counts & total scores for MCFold

2. Individual counts for MCFold [ download as .csv ]