ID	Duplex structure	Position	Score	MFE
1	miRNA 3' cgAGAAAAGUAAUUACAUCUGu 5' ||||||| || || |||| Target 5' ttTCTTTTC-TTTTTG-AGACc 3'	87 - 106	119.00	-10.90
2	miRNA 3' cgAGAAAAGUAAUU-------ACAUCUGu 5' ||| | || |: || |||| Target 5' ccTCTCTCCAGCAGGAAGGGCTGCAGACt 3'	484 - 512	112.00	-10.40
3	miRNA 3' cgaGAAAAGUAAUUA-CAUCUgu 5' :||| :||| | ||||| Target 5' tgaTTTTGTATTTTTAGTAGAga 3'	247 - 269	111.00	-6.00

Mutant ID	Mutant Position	Mutant Source
COSN22337415	11	COSMIC
COSN30137645	38	COSMIC
COSN27046342	64	COSMIC
COSN30172244	77	COSMIC
COSN15279431	385	COSMIC
COSN22372207	652	COSMIC
rs12937692	673	GWAS

Mutant ID	Mutant Position	Mutant Source
rs753116195	2	dbSNP
rs753851123	2	dbSNP
rs754500086	4	dbSNP
rs1410870503	8	dbSNP
rs778609170	9	dbSNP
rs1371882928	13	dbSNP
rs889871035	17	dbSNP
rs747737024	18	dbSNP
rs375748291	20	dbSNP
rs1358924079	21	dbSNP
rs781409238	23	dbSNP
rs1179582384	25	dbSNP
rs746181286	27	dbSNP
rs369351726	34	dbSNP
rs201560232	35	dbSNP
rs763489064	37	dbSNP
rs768697582	41	dbSNP
rs200826931	42	dbSNP
rs1384090672	43	dbSNP
rs1442351143	44	dbSNP
rs1237276561	50	dbSNP
rs761936185	51	dbSNP
rs757065458	52	dbSNP
rs369725603	53	dbSNP
rs1380801742	57	dbSNP
rs1228213216	59	dbSNP
rs533182118	64	dbSNP
rs1180396577	65	dbSNP
rs909214511	72	dbSNP
rs941890890	77	dbSNP
rs990981243	80	dbSNP
rs1473231030	84	dbSNP
rs1398158336	91	dbSNP
rs1165122298	94	dbSNP
rs147737256	96	dbSNP
rs916718970	101	dbSNP
rs1382797976	106	dbSNP
rs1164946952	111	dbSNP
rs967805763	118	dbSNP
rs1379685607	121	dbSNP
rs551504997	122	dbSNP
rs1439389840	124	dbSNP
rs1251015250	127	dbSNP
rs560598270	128	dbSNP
rs1196556527	129	dbSNP
rs1286178474	133	dbSNP
rs527787722	145	dbSNP
rs549158059	146	dbSNP
rs746053107	148	dbSNP
rs567509207	152	dbSNP
rs1221002091	153	dbSNP
rs1237296283	166	dbSNP
rs931879773	174	dbSNP
rs531622744	175	dbSNP
rs1203501527	176	dbSNP
rs770060547	177	dbSNP
rs1363333369	179	dbSNP
rs887582156	186	dbSNP
rs1359795313	187	dbSNP
rs1005608899	189	dbSNP
rs1038398602	196	dbSNP
rs550130290	202	dbSNP
rs1471134357	204	dbSNP
rs1189871934	208	dbSNP
rs775429973	209	dbSNP
rs144711933	211	dbSNP
rs1052661146	214	dbSNP
rs896741426	218	dbSNP
rs749327334	219	dbSNP
rs1023829948	222	dbSNP
rs968192566	225	dbSNP
rs1169243490	228	dbSNP
rs1283689395	229	dbSNP
rs769060341	229	dbSNP
rs538596484	233	dbSNP
rs956438053	234	dbSNP
rs1390739829	238	dbSNP
rs1223346988	242	dbSNP
rs1343237303	255	dbSNP
rs1284853949	268	dbSNP
rs976157351	270	dbSNP
rs1007654432	272	dbSNP
rs1402309792	280	dbSNP
rs1385665870	293	dbSNP
rs1016244346	301	dbSNP
rs553500278	306	dbSNP
rs1427423879	307	dbSNP
rs963390618	316	dbSNP
rs1480899391	317	dbSNP
rs1241531211	318	dbSNP
rs147833434	326	dbSNP
rs536007274	339	dbSNP
rs1263115592	340	dbSNP
rs1203406176	352	dbSNP
rs1321901629	357	dbSNP
rs960143502	361	dbSNP
rs909073576	364	dbSNP
rs543766636	365	dbSNP
rs948470054	366	dbSNP
rs774874599	371	dbSNP
rs116243986	372	dbSNP
rs1336046194	373	dbSNP
rs573927298	378	dbSNP
rs1450397860	384	dbSNP
rs745777987	387	dbSNP
rs544481546	405	dbSNP
rs189533106	406	dbSNP
rs1419157327	409	dbSNP
rs577930824	414	dbSNP
rs930035465	435	dbSNP
rs1183471696	438	dbSNP
rs536872607	438	dbSNP
rs1226819834	441	dbSNP
rs1251169752	443	dbSNP
rs998177289	451	dbSNP
rs896464399	460	dbSNP
rs1254359375	462	dbSNP
rs1313764069	463	dbSNP
rs73316154	467	dbSNP
rs759173914	468	dbSNP
rs1441281011	472	dbSNP
rs1354134476	476	dbSNP
rs1327146059	478	dbSNP
rs560332064	484	dbSNP
rs1390805811	490	dbSNP
rs1163016808	491	dbSNP
rs963360088	514	dbSNP
rs1001032550	515	dbSNP
rs1031130293	523	dbSNP
rs956668334	527	dbSNP
rs764793258	529	dbSNP
rs527777634	531	dbSNP
rs752152358	532	dbSNP
rs986038893	535	dbSNP
rs909123959	537	dbSNP
rs1372368274	538	dbSNP
rs959950107	540	dbSNP
rs542789594	544	dbSNP
rs1219700630	547	dbSNP
rs561043534	556	dbSNP
rs1174064322	564	dbSNP
rs1315700502	565	dbSNP
rs1222961701	567	dbSNP
rs941905088	577	dbSNP
rs531508777	586	dbSNP
rs1444555895	587	dbSNP
rs1371481664	588	dbSNP
rs993167999	591	dbSNP
rs1422875028	595	dbSNP
rs1451432451	597	dbSNP
rs919071125	604	dbSNP
rs550018602	608	dbSNP
rs1320711634	614	dbSNP
rs193201576	621	dbSNP
rs969890777	624	dbSNP
rs1472710542	626	dbSNP
rs1366733609	628	dbSNP
rs1196616949	629	dbSNP
rs1432177248	640	dbSNP
rs930072505	644	dbSNP
rs1291905055	649	dbSNP
rs1214921674	651	dbSNP
rs1315064703	653	dbSNP
rs978470729	657	dbSNP
rs1295512460	659	dbSNP
rs1224191364	660	dbSNP
rs1351320445	661	dbSNP
rs925740905	663	dbSNP
rs796310885	665	dbSNP
rs896519366	672	dbSNP
rs922267240	672	dbSNP
rs12937692	673	dbSNP
rs551598836	678	dbSNP
rs1161715912	687	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.