CompaRNA - on-line benchmarks of RNA structure prediction methods

Laboratory of Structural Bioinformatics @ Adam Mickiewicz University in Poznan

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Overview

Metric	MaxExpect		McQFold
MCC	0.615	>	0.519
Average MCC ± 95% Confidence Intervals	0.690 ± 0.060	>	0.677 ± 0.059
Sensitivity	0.538	>	0.445
Positive Predictive Value	0.704	>	0.606
Total TP	1983	>	1640
Total TN	4426311	<	4426421
Total FP	959	<	1156
Total FP CONTRA	92	<	112
Total FP INCONS	743	<	956
Total FP COMP	124	>	88
Total FN	1702	<	2045
P-value	3.56938820447e-08

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Performance plots

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Performance of MaxExpect - scored higher in this pairwise comparison

1. Total counts & total scores for MaxExpect

Total Base Pair Counts
Total TP	1983
Total TN	4426311
Total FP	959
Total FP CONTRA	92
Total FP INCONS	743
Total FP COMP	124
Total FN	1702

Total Scores
MCC	0.615
Average MCC ± 95% Confidence Intervals	0.690 ± 0.060
Sensitivity	0.538
Positive Predictive Value	0.704
Nr of predictions	98

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

RNA Chain	Rfam family	MCC	SENS	PPV	TP	TN	FP	FP CONTRA	FP INCONS	FP COMP	FN
2KD8_A	-	1.00	1.00	1.00	9	222	0	0	0	0	0
2KE6_A	K10_TLS links to Rfam database...	0.92	0.89	0.94	17	1110	2	0	1	1	2
2KPV_A	-	0.96	0.92	1.00	12	549	0	0	0	0	1
2KRL_A	-	0.76	0.60	0.96	24	5126	5	0	1	4	16
2KU0_A	-	-0.02	0.00	0.00	0	694	9	0	9	0	16
2KUR_A	K10_TLS links to Rfam database...	0.90	0.86	0.95	18	1109	1	0	1	0	3
2KUU_A	K10_TLS links to Rfam database...	0.87	0.81	0.94	17	1110	2	0	1	1	4
2KUV_A	K10_TLS links to Rfam database...	0.88	0.82	0.95	18	1109	1	0	1	0	4
2KUW_A	K10_TLS links to Rfam database...	0.90	0.86	0.95	18	1109	1	0	1	0	3
2KX8_A	7SK links to Rfam database...	0.94	0.89	1.00	16	845	0	0	0	0	2
2KXM_A	-	0.83	0.70	1.00	7	344	0	0	0	0	3
2KZL_A	-	0.86	0.74	1.00	14	1471	0	0	0	0	5
2L1F_B	Gammaretro_CES links to Rfam database...	0.98	0.96	1.00	24	2121	0	0	0	0	1
2L1F_A	Gammaretro_CES links to Rfam database...	0.98	0.96	1.00	23	2057	0	0	0	0	1
2L2K_A	-	0.94	0.89	1.00	17	844	0	0	0	0	2
2L3C_B	-	0.91	0.82	1.00	14	547	0	0	0	0	3
2L3E_A	-	0.96	0.92	1.00	12	583	1	0	0	1	1
2L3J_B	mir-2985-2 links to Rfam database...	0.94	0.88	1.00	30	2455	0	0	0	0	4
2L5Z_A	-	0.86	0.75	1.00	9	316	0	0	0	0	3
2L94_A	HIV_FE links to Rfam database...	0.97	0.95	1.00	19	971	0	0	0	0	1
2LA5_A	-	0.39	0.26	0.63	5	622	3	1	2	0	14
2LBS_A	-	1.00	1.00	1.00	14	482	0	0	0	0	0
2LC8_A	GP_knot1 links to Rfam database...	-0.01	0.00	0.00	0	1525	15	2	13	0	20
2LDL_A	-	0.90	0.82	1.00	9	342	1	0	0	1	2
2LDT_A	-	0.85	0.73	1.00	11	454	0	0	0	0	4
2LHP_A	-	0.97	0.94	1.00	15	651	0	0	0	0	1
2LJJ_A	-	1.00	1.00	1.00	8	343	2	0	0	2	0
2LK3_A	-	0.95	0.90	1.00	9	267	0	0	0	0	1
2LKR_A	-	0.81	0.74	0.88	29	6072	6	0	4	2	10
2LQZ_A	-	0.85	0.82	0.90	9	341	1	1	0	0	2
2LWK_A	-	0.88	0.85	0.92	11	484	1	0	1	0	2
2RRC_A	-	0.70	0.50	1.00	5	226	0	0	0	0	5
2WRQ_Y	tRNA links to Rfam database...	0.53	0.53	0.53	9	2833	13	5	3	5	8
2WW9_D	-	0.14	0.12	0.19	3	1937	13	0	13	0	23
2WW9_F	-	0.69	0.70	0.70	7	290	3	0	3	0	3
2WW9_E	-	-0.01	0.00	0.00	0	556	5	0	5	0	14
2WWQ_V	tRNA links to Rfam database...	0.76	0.64	0.90	18	2906	3	0	2	1	10
2XKV_B	Bacteria_small_SRP links to Rfam database...	0.51	0.50	0.53	10	4541	24	0	9	15	10
2XQD_Y	tRNA links to Rfam database...	0.88	0.78	1.00	21	2829	0	0	0	0	6
2XXA_G	Bacteria_small_SRP links to Rfam database...	0.25	0.24	0.27	10	5114	27	1	26	0	32
2Y8W_B	-	1.00	1.00	1.00	6	184	1	0	0	1	0
2Y9C_V	-	0.65	0.63	0.68	15	2256	8	1	6	1	9
2YIE_X	-	0.36	0.33	0.40	4	1368	6	2	4	0	8
2YIE_Z	-	-0.01	0.00	0.00	0	1525	15	3	12	0	12
3A2K_C	tRNA links to Rfam database...	0.42	0.39	0.46	11	2902	13	2	11	0	17
3ADB_C	-	0.80	0.74	0.88	28	4154	4	0	4	0	10
3AKZ_H	tRNA links to Rfam database...	0.84	0.75	0.95	21	2679	1	1	0	0	7
3AM1_B	-	0.78	0.71	0.86	25	3211	4	0	4	0	10
3AMU_B	tRNA links to Rfam database...	0.64	0.59	0.70	16	2980	9	0	7	2	11
3GX2_A	SAM links to Rfam database...	0.77	0.63	0.96	25	4345	2	0	1	1	15
3IAB_R	-	0.92	0.86	1.00	12	1023	0	0	0	0	2
3IVN_B	Purine links to Rfam database...	0.78	0.61	1.00	19	2327	0	0	0	0	12
3IWN_A	c-di-GMP-I links to Rfam database...	0.74	0.67	0.81	22	4251	6	0	5	1	11
3IYQ_A	tmRNA links to Rfam database...	0.29	0.31	0.27	29	60617	84	19	61	4	65
3IZ4_A	tmRNA links to Rfam database...	0.54	0.46	0.64	61	70781	39	3	31	5	71
3IZF_C	5S_rRNA links to Rfam database...	0.71	0.61	0.83	33	6863	7	1	6	0	21
3J0L_7	-	-0.01	0.00	0.00	0	1213	12	0	12	0	17
3J0L_8	-	0.93	0.88	1.00	7	183	0	0	0	0	1
3J0L_a	-	0.39	0.31	0.50	5	1118	5	2	3	0	11
3J0L_1	-	0.76	0.63	0.92	12	1212	2	0	1	1	7
3J0L_h	-	0.81	0.65	1.00	28	6077	2	0	0	2	15
3J0L_g	-	-0.01	0.00	0.00	0	461	4	1	3	0	4
3J0L_2	-	0.25	0.24	0.26	8	6185	25	2	21	2	25
3J16_L	tRNA links to Rfam database...	0.29	0.23	0.37	7	2756	12	0	12	0	23
3JYV_7	tRNA links to Rfam database...	0.41	0.31	0.56	10	2832	8	0	8	0	22
3JYX_4	5_8S_rRNA links to Rfam database...	0.31	0.30	0.31	10	12214	34	4	18	12	23
3JYX_3	5S_rRNA links to Rfam database...	0.64	0.63	0.65	17	6302	19	1	8	10	10
3KIY_A	-	0.54	0.45	0.65	553	4053271	314	23	281	10	688
3KTW_C	-	0.54	0.47	0.65	20	4529	12	2	9	1	23
3LA5_A	Purine links to Rfam database...	0.78	0.62	1.00	21	2464	0	0	0	0	13
3NDB_M	-	0.78	0.69	0.89	42	9133	6	0	5	1	19
3NKB_B	-	0.59	0.54	0.67	14	1995	7	0	7	0	12
3NMU_E	-	-0.01	0.00	0.00	0	553	10	1	7	2	6
3NPB_A	SAM links to Rfam database...	0.71	0.61	0.82	28	6987	9	0	6	3	18
3O58_3	5_8S_rRNA links to Rfam database...	0.35	0.34	0.35	12	12369	35	2	20	13	23
3O58_2	5S_rRNA links to Rfam database...	0.75	0.76	0.74	29	7221	11	3	7	1	9
3OVB_D	-	1.00	1.00	1.00	11	584	1	0	0	1	0
3OVS_D	-	0.96	0.92	1.00	12	549	0	0	0	0	1
3P22_G	-	0.96	0.92	1.00	11	730	0	0	0	0	1
3PDR_A	ykoK links to Rfam database...	0.76	0.63	0.94	45	12832	5	0	3	2	27
3R4F_A	-	0.96	0.92	1.00	23	2122	0	0	0	0	2
3R9X_C	-	0.84	0.80	0.89	8	586	2	0	1	1	2
3RKF_A	Purine links to Rfam database...	0.76	0.59	1.00	20	2191	0	0	0	0	14
3SD1_A	THF links to Rfam database...	0.58	0.48	0.71	20	3888	8	1	7	0	22
3SIU_F	-	0.85	0.73	1.00	8	370	0	0	0	0	3
3SN2_B	IRE_II links to Rfam database...	1.00	1.00	1.00	12	394	0	0	0	0	0
3TRZ_Z	-	0.91	0.83	1.00	5	205	1	0	0	1	1
3TS0_U	-	1.00	1.00	1.00	6	247	1	0	0	1	0
3TS2_V	-	1.00	1.00	1.00	5	271	0	0	0	0	0
3U4M_B	-	0.45	0.35	0.59	13	3138	9	1	8	0	24
3UZL_B	tRNA links to Rfam database...	0.77	0.62	0.96	23	3546	1	0	1	0	14
3VJR_D	-	0.96	0.92	1.00	12	618	0	0	0	0	1
4A1C_3	5S_rRNA links to Rfam database...	0.69	0.57	0.84	31	7103	6	0	6	0	23
4A1C_2	5_8S_rRNA links to Rfam database...	0.14	0.15	0.14	5	11746	41	4	26	11	28
4A4U_A	-	1.00	1.00	1.00	9	222	0	0	0	0	0
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...	0.76	0.58	1.00	11	1264	0	0	0	0	8
4ENC_A	crcB links to Rfam database...	0.31	0.26	0.38	5	1313	8	1	7	0	14

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Performance of McQFold - scored lower in this pairwise comparison

1. Total counts & total scores for McQFold

Total Base Pair Counts
Total TP	1640
Total TN	4426421
Total FP	1156
Total FP CONTRA	112
Total FP INCONS	956
Total FP COMP	88
Total FN	2045

Total Scores
MCC	0.519
Average MCC ± 95% Confidence Intervals	0.677 ± 0.059
Sensitivity	0.445
Positive Predictive Value	0.606
Nr of predictions	98

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

RNA Chain	Rfam family	MCC	SENS	PPV	TP	TN	FP	FP CONTRA	FP INCONS	FP COMP	FN
2KD8_A	-	1.00	1.00	1.00	9	222	1	0	0	1	0
2KE6_A	K10_TLS links to Rfam database...	0.89	0.79	1.00	15	1113	1	0	0	1	4
2KPV_A	-	0.96	0.92	1.00	12	549	0	0	0	0	1
2KRL_A	-	0.59	0.53	0.68	21	5120	13	3	7	3	19
2KU0_A	-	0.75	0.56	1.00	9	694	0	0	0	0	7
2KUR_A	K10_TLS links to Rfam database...	0.87	0.76	1.00	16	1112	0	0	0	0	5
2KUU_A	K10_TLS links to Rfam database...	0.84	0.71	1.00	15	1113	1	0	0	1	6
2KUV_A	K10_TLS links to Rfam database...	0.85	0.73	1.00	16	1112	0	0	0	0	6
2KUW_A	K10_TLS links to Rfam database...	0.87	0.76	1.00	16	1112	0	0	0	0	5
2KX8_A	7SK links to Rfam database...	0.88	0.83	0.94	15	845	1	0	1	0	3
2KXM_A	-	0.70	0.50	1.00	5	346	0	0	0	0	5
2KZL_A	-	0.86	0.74	1.00	14	1471	1	0	0	1	5
2L1F_B	Gammaretro_CES links to Rfam database...	0.98	0.96	1.00	24	2121	0	0	0	0	1
2L1F_A	Gammaretro_CES links to Rfam database...	0.98	0.96	1.00	23	2057	0	0	0	0	1
2L2K_A	-	0.97	0.95	1.00	18	843	0	0	0	0	1
2L3C_B	-	0.94	0.88	1.00	15	546	0	0	0	0	2
2L3E_A	-	1.00	1.00	1.00	13	582	1	0	0	1	0
2L3J_B	mir-2985-2 links to Rfam database...	0.89	0.79	1.00	27	2458	0	0	0	0	7
2L5Z_A	-	0.86	0.75	1.00	9	316	0	0	0	0	3
2L94_A	HIV_FE links to Rfam database...	0.97	0.95	1.00	19	971	0	0	0	0	1
2LA5_A	-	0.46	0.26	0.83	5	624	1	0	1	0	14
2LBS_A	-	1.00	1.00	1.00	14	482	1	0	0	1	0
2LC8_A	GP_knot1 links to Rfam database...	0.61	0.55	0.69	11	1524	5	0	5	0	9
2LDL_A	-	0.73	0.55	1.00	6	345	0	0	0	0	5
2LDT_A	-	0.68	0.47	1.00	7	458	0	0	0	0	8
2LHP_A	-	1.00	1.00	1.00	16	650	0	0	0	0	0
2LJJ_A	-	1.00	1.00	1.00	8	343	2	0	0	2	0
2LK3_A	-	0.95	0.90	1.00	9	267	0	0	0	0	1
2LKR_A	-	0.51	0.46	0.58	18	6074	13	2	11	0	21
2LQZ_A	-	0.91	0.91	0.91	10	340	1	1	0	0	1
2LWK_A	-	0.83	0.77	0.91	10	485	2	0	1	1	3
2RRC_A	-	0.70	0.50	1.00	5	226	0	0	0	0	5
2WRQ_Y	tRNA links to Rfam database...	0.57	0.59	0.56	10	2832	13	5	3	5	7
2WW9_D	-	0.32	0.23	0.46	6	1940	7	2	5	0	20
2WW9_F	-	0.71	0.60	0.86	6	293	1	0	1	0	4
2WW9_E	-	-0.01	0.00	0.00	0	556	5	0	5	0	14
2WWQ_V	tRNA links to Rfam database...	0.00	0.00	0.00	0	2926	0	0	0	0	28
2XKV_B	Bacteria_small_SRP links to Rfam database...	0.31	0.30	0.33	6	4542	25	1	11	13	14
2XQD_Y	tRNA links to Rfam database...	0.88	0.78	1.00	21	2829	0	0	0	0	6
2XXA_G	Bacteria_small_SRP links to Rfam database...	0.27	0.24	0.32	10	5120	21	0	21	0	32
2Y8W_B	-	1.00	1.00	1.00	6	184	2	0	0	2	0
2Y9C_V	-	0.59	0.54	0.65	13	2258	8	1	6	1	11
2YIE_X	-	0.36	0.33	0.40	4	1368	6	2	4	0	8
2YIE_Z	-	0.43	0.42	0.45	5	1529	6	3	3	0	7
3A2K_C	tRNA links to Rfam database...	0.86	0.75	1.00	21	2905	0	0	0	0	7
3ADB_C	-	0.92	0.84	1.00	32	4154	1	0	0	1	6
3AKZ_H	tRNA links to Rfam database...	0.68	0.61	0.77	17	2679	6	1	4	1	11
3AM1_B	-	0.91	0.83	1.00	29	3211	1	0	0	1	6
3AMU_B	tRNA links to Rfam database...	0.75	0.59	0.94	16	2986	3	0	1	2	11
3GX2_A	SAM links to Rfam database...	0.47	0.40	0.57	16	4343	13	1	11	1	24
3IAB_R	-	0.92	0.86	1.00	12	1023	0	0	0	0	2
3IVN_B	Purine links to Rfam database...	0.78	0.61	1.00	19	2327	0	0	0	0	12
3IWN_A	c-di-GMP-I links to Rfam database...	0.20	0.18	0.24	6	4253	19	2	17	0	27
3IYQ_A	tmRNA links to Rfam database...	0.28	0.31	0.26	29	60614	87	19	64	4	65
3IZ4_A	tmRNA links to Rfam database...	0.42	0.36	0.49	47	70780	53	6	43	4	85
3IZF_C	5S_rRNA links to Rfam database...	0.68	0.56	0.83	30	6867	6	0	6	0	24
3J0L_7	-	-0.01	0.00	0.00	0	1215	10	0	10	0	17
3J0L_8	-	0.93	0.88	1.00	7	183	0	0	0	0	1
3J0L_a	-	0.26	0.19	0.38	3	1120	5	1	4	0	13
3J0L_1	-	0.65	0.47	0.90	9	1215	3	0	1	2	10
3J0L_h	-	0.65	0.49	0.88	21	6081	3	0	3	0	22
3J0L_g	-	-0.01	0.00	0.00	0	461	4	1	3	0	4
3J0L_2	-	0.26	0.24	0.30	8	6189	21	0	19	2	25
3J16_L	tRNA links to Rfam database...	0.75	0.57	1.00	17	2758	0	0	0	0	13
3JYV_7	tRNA links to Rfam database...	-0.01	0.00	0.00	0	2830	20	0	20	0	32
3JYX_4	5_8S_rRNA links to Rfam database...	0.20	0.21	0.19	7	12210	33	8	21	4	26
3JYX_3	5S_rRNA links to Rfam database...	0.21	0.22	0.20	6	6298	24	9	15	0	21
3KIY_A	-	0.31	0.26	0.38	317	4053291	529	22	498	9	924
3KTW_C	-	0.36	0.30	0.45	13	4531	17	1	15	1	30
3LA5_A	Purine links to Rfam database...	0.78	0.62	1.00	21	2464	0	0	0	0	13
3NDB_M	-	0.81	0.70	0.93	43	9134	4	1	2	1	18
3NKB_B	-	0.36	0.31	0.44	8	1998	10	1	9	0	18
3NMU_E	-	0.41	0.17	1.00	1	560	3	0	0	3	5
3NPB_A	SAM links to Rfam database...	0.81	0.67	0.97	31	6989	4	1	0	3	15
3O58_3	5_8S_rRNA links to Rfam database...	0.26	0.26	0.26	9	12368	26	10	16	0	26
3O58_2	5S_rRNA links to Rfam database...	0.83	0.71	0.96	27	7232	2	0	1	1	11
3OVB_D	-	1.00	1.00	1.00	11	584	1	0	0	1	0
3OVS_D	-	0.96	0.92	1.00	12	549	0	0	0	0	1
3P22_G	-	0.96	0.92	1.00	11	730	0	0	0	0	1
3PDR_A	ykoK links to Rfam database...	0.69	0.56	0.87	40	12834	9	0	6	3	32
3R4F_A	-	0.96	0.92	1.00	23	2122	1	0	0	1	2
3R9X_C	-	0.84	0.80	0.89	8	586	2	0	1	1	2
3RKF_A	Purine links to Rfam database...	0.76	0.59	1.00	20	2191	0	0	0	0	14
3SD1_A	THF links to Rfam database...	0.71	0.60	0.86	25	3887	4	0	4	0	17
3SIU_F	-	0.73	0.55	1.00	6	372	0	0	0	0	5
3SN2_B	IRE_II links to Rfam database...	0.96	0.92	1.00	11	395	0	0	0	0	1
3TRZ_Z	-	0.91	0.83	1.00	5	205	2	0	0	2	1
3TS0_U	-	1.00	1.00	1.00	6	247	1	0	0	1	0
3TS2_V	-	1.00	1.00	1.00	5	271	0	0	0	0	0
3U4M_B	-	0.73	0.57	0.95	21	3138	1	0	1	0	16
3UZL_B	tRNA links to Rfam database...	0.45	0.41	0.52	15	3541	14	0	14	0	22
3VJR_D	-	0.96	0.92	1.00	12	618	0	0	0	0	1
4A1C_3	5S_rRNA links to Rfam database...	0.25	0.22	0.29	12	7099	29	1	28	0	42
4A1C_2	5_8S_rRNA links to Rfam database...	0.15	0.15	0.15	5	11748	33	5	23	5	28
4A4U_A	-	1.00	1.00	1.00	9	222	0	0	0	0	0
4AOB_A	SAM links to Rfam database...	0.42	0.33	0.54	14	4345	13	1	11	1	28
4ENB_A	crcB links to Rfam database...	0.89	0.79	1.00	15	1260	0	0	0	0	4
4ENC_A	crcB links to Rfam database...	0.86	0.79	0.94	15	1310	1	1	0	0	4

^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 MaxExpect - scored higher in this pairwise comparison

1. Total counts & total scores for MaxExpect

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

Performance of McQFold - scored lower in this pairwise comparison

1. Total counts & total scores for McQFold

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