ID	Duplex structure	Position	Score	MFE
1	miRNA 3' gggucUCGAC--UCG-GGUGUc 5' | :|| :|| ||||| Target 5' catgcATTTGTAGGCACCACAa 3'	323 - 344	112.00	-8.40
2	miRNA 3' gggucucgacuCGGGUGUc 5' | ||||| Target 5' aggctttccttGGCCACAg 3'	32 - 50	108.00	-13.90
3	miRNA 3' ggGUCUCGACUCGGGUGUc 5' :||| || |:|:|:| Target 5' gcTAGA-ATGTGTCTATAg 3'	372 - 389	104.00	-15.40

Mutant ID	Mutant Position	Mutant Source
COSN26679116	8	COSMIC
COSN16131253	14	COSMIC
COSN31499390	16	COSMIC
COSN30491509	22	COSMIC
COSN30453687	27	COSMIC
COSN165981	33	COSMIC
COSN8407689	60	COSMIC
COSN30450975	64	COSMIC
COSN31586301	87	COSMIC
COSN31570078	101	COSMIC
COSN31613296	131	COSMIC
COSN30512790	138	COSMIC
COSN30450270	150	COSMIC
COSN31507371	189	COSMIC
COSN6147625	416	COSMIC

Mutant ID	Mutant Position	Mutant Source
rs777195119	2	dbSNP
rs866222096	3	dbSNP
rs1257455097	6	dbSNP
rs1485530303	7	dbSNP
rs1185816810	8	dbSNP
rs768237279	9	dbSNP
rs748842060	13	dbSNP
rs779782195	15	dbSNP
rs1209433577	18	dbSNP
rs769340325	18	dbSNP
rs745590282	19	dbSNP
rs777992527	21	dbSNP
rs758835669	22	dbSNP
rs1176695723	23	dbSNP
rs377227740	23	dbSNP
rs1405833943	24	dbSNP
rs1234579916	26	dbSNP
rs2287832	33	dbSNP
rs753927619	38	dbSNP
rs766540802	40	dbSNP
rs1446011906	41	dbSNP
rs200640694	45	dbSNP
rs767197418	51	dbSNP
rs1048574758	52	dbSNP
rs1295972332	57	dbSNP
rs1374853272	60	dbSNP
rs1476528058	62	dbSNP
rs542986968	63	dbSNP
rs894542807	67	dbSNP
rs750980002	69	dbSNP
rs577519559	70	dbSNP
rs557591892	72	dbSNP
rs1232565017	76	dbSNP
rs752016279	83	dbSNP
rs1486302448	85	dbSNP
rs1042695302	87	dbSNP
rs1204379187	88	dbSNP
rs1231299330	93	dbSNP
rs945300486	96	dbSNP
rs915063273	98	dbSNP
rs1252626241	103	dbSNP
rs766905800	107	dbSNP
rs989283798	111	dbSNP
rs953876990	115	dbSNP
rs957886015	115	dbSNP
rs1395409181	121	dbSNP
rs1409357704	125	dbSNP
rs1168199383	126	dbSNP
rs1355839360	136	dbSNP
rs1442280006	149	dbSNP
rs1292373929	151	dbSNP
rs920974589	154	dbSNP
rs534607860	159	dbSNP
rs976534823	161	dbSNP
rs565893705	163	dbSNP
rs1419895079	164	dbSNP
rs1214540111	167	dbSNP
rs1277428330	169	dbSNP
rs1015297469	170	dbSNP
rs1309721143	171	dbSNP
rs1205315728	172	dbSNP
rs763412952	176	dbSNP
rs1252411369	184	dbSNP
rs1342494156	185	dbSNP
rs952938864	188	dbSNP
rs1027213906	189	dbSNP
rs1184768137	195	dbSNP
rs1421581103	197	dbSNP
rs555256157	210	dbSNP
rs1013001810	212	dbSNP
rs1013570220	218	dbSNP
rs536764031	220	dbSNP
rs1388840902	227	dbSNP
rs1462733598	235	dbSNP
rs1036175897	236	dbSNP
rs1002999018	242	dbSNP
rs567732212	246	dbSNP
rs550995041	252	dbSNP
rs537400519	253	dbSNP
rs116612558	255	dbSNP
rs1364739087	256	dbSNP
rs887954176	259	dbSNP
rs893703836	265	dbSNP
rs1050996308	270	dbSNP
rs1053706213	271	dbSNP
rs765577586	274	dbSNP
rs932264732	278	dbSNP
rs1274023185	281	dbSNP
rs1446579235	284	dbSNP
rs932437296	291	dbSNP
rs921138899	293	dbSNP
rs773321347	297	dbSNP
rs1475712713	302	dbSNP
rs1432309026	307	dbSNP
rs1187111140	308	dbSNP
rs943824838	314	dbSNP
rs769823600	316	dbSNP
rs1475899222	317	dbSNP
rs552100707	322	dbSNP
rs1488660297	332	dbSNP
rs1398552656	334	dbSNP
rs1040708890	339	dbSNP
rs1196723600	342	dbSNP
rs982391213	347	dbSNP
rs762090724	348	dbSNP
rs1027161542	349	dbSNP
rs1353709933	354	dbSNP
rs531028782	356	dbSNP
rs991736230	362	dbSNP
rs959125133	363	dbSNP
rs1258870152	365	dbSNP
rs1203564200	379	dbSNP
rs987907794	380	dbSNP
rs1447331062	383	dbSNP
rs1210157698	384	dbSNP
rs1035887712	387	dbSNP
rs1255337514	389	dbSNP
rs1329576433	391	dbSNP
rs1486574475	406	dbSNP
rs370923096	412	dbSNP
rs1003357321	414	dbSNP
rs1468327925	415	dbSNP
rs768846148	415	dbSNP
rs1159909746	416	dbSNP
rs925149909	417	dbSNP
rs1420682446	427	dbSNP
rs980986934	430	dbSNP
rs969313345	432	dbSNP
rs903237414	433	dbSNP
rs776731006	436	dbSNP
rs189049557	438	dbSNP
rs1481705554	442	dbSNP
rs549276137	444	dbSNP
rs1467698807	449	dbSNP
rs1053694994	454	dbSNP
rs1233301226	456	dbSNP
rs183556262	462	dbSNP
rs1349991085	467	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.