ID	Duplex structure	Position	Score	MFE
1	miRNA 3' ugacccaaguggaaaUUCCCGu 5' |||||| Target 5' tttagaacatatataAAGGGCa 3'	179 - 200	120.00	-11.20
2	miRNA 3' ugACCCAAGUG--GAAAUUCCCGu 5' |||| |||| | |||| | Target 5' ggTGGG-TCACAGC-AAAAGGACc 3'	89 - 110	92.00	-12.60
3	miRNA 3' ugacccaaguggaaauuCCCGu 5' |||| Target 5' cgagcgaggcactcactGGGCa 3'	32 - 53	80.00	-11.30

Mutant ID	Mutant Position	Mutant Source
COSN8865581	3	COSMIC
COSN30148503	6	COSMIC
COSN1182963	10	COSMIC
COSN30155885	38	COSMIC
COSN30178062	43	COSMIC
COSN30149275	66	COSMIC
COSN30486010	88	COSMIC
COSN31500803	89	COSMIC
COSN31554859	126	COSMIC
COSN6079474	242	COSMIC

Mutant ID	Mutant Position	Mutant Source
rs386788939	2	dbSNP
rs11716	3	dbSNP
rs2233543	4	dbSNP
rs1039207477	5	dbSNP
rs527993353	7	dbSNP
rs923003592	12	dbSNP
rs1309013765	19	dbSNP
rs767967750	21	dbSNP
rs1394773842	22	dbSNP
rs920620743	26	dbSNP
rs185648760	33	dbSNP
rs376901396	34	dbSNP
rs564302332	37	dbSNP
rs757236292	38	dbSNP
rs1204265718	43	dbSNP
rs778997931	46	dbSNP
rs1481605048	49	dbSNP
rs879057877	51	dbSNP
rs1363353944	53	dbSNP
rs1399001019	63	dbSNP
rs774868931	70	dbSNP
rs939837291	72	dbSNP
rs1046300600	73	dbSNP
rs906355039	74	dbSNP
rs1166556649	76	dbSNP
rs1002389242	77	dbSNP
rs1367835881	78	dbSNP
rs1185245857	82	dbSNP
rs1439380316	83	dbSNP
rs533400522	85	dbSNP
rs550291329	87	dbSNP
rs190573534	88	dbSNP
rs146511825	89	dbSNP
rs1357071126	90	dbSNP
rs1025036731	91	dbSNP
rs1243201372	92	dbSNP
rs1175504018	97	dbSNP
rs1337923174	100	dbSNP
rs556101446	102	dbSNP
rs1021171745	107	dbSNP
rs1467582828	110	dbSNP
rs770683206	111	dbSNP
rs906621944	113	dbSNP
rs1302905351	117	dbSNP
rs1461516202	117	dbSNP
rs1371998465	123	dbSNP
rs966896387	128	dbSNP
rs987680805	129	dbSNP
rs994332044	142	dbSNP
rs1019106946	146	dbSNP
rs964835984	147	dbSNP
rs1437573402	157	dbSNP
rs1223256526	158	dbSNP
rs15379	159	dbSNP
rs1314451230	163	dbSNP
rs535894389	174	dbSNP
rs1802953	179	dbSNP
rs1452285959	189	dbSNP
rs1289177412	194	dbSNP
rs1211459366	206	dbSNP
rs141048997	219	dbSNP
rs930646891	226	dbSNP
rs983431789	234	dbSNP
rs907872136	236	dbSNP
rs1482133639	238	dbSNP
rs181737616	242	dbSNP

- Nature methods, 2011

Cross-linking and immunoprecipitation (CLIP) is increasingly used to map transcriptome-wide binding sites of RNA-binding proteins. We developed a method for CLIP data analysis, and applied it to compare CLIP with photoactivatable ribonucleoside-enhanced CLIP (PAR-CLIP) and to uncover how differences in cross-linking and ribonuclease digestion affect the identified sites. We found only small differences in accuracies of these methods in identifying binding sites of HuR, which binds low-complexity sequences, and Argonaute 2, which has a complex binding specificity. We found that cross-link-induced mutations led to single-nucleotide resolution for both PAR-CLIP and CLIP. Our results confirm the expectation from original CLIP publications that RNA-binding proteins do not protect their binding sites sufficiently under the denaturing conditions used during the CLIP procedure, and we show that extensive digestion with sequence-specific RNases strongly biases the recovered binding sites. This bias can be substantially reduced by milder nuclease digestion conditions.