>APIP|NM_015957|3'UTR
   1 GCCAAAAGAAAGTCTAATTATATACAGAGATAAAGCTAAACGTAATTATTATTTAAATGAAAGCTATTTTTTTAAATGAA
  81 TTGAAATTTTTCATGATGCTACTAATTTGCCACTAAATACTGCAAATGGTCACCCTGAATCTCTTCTGACATTGGATGTT
 161 ATTTGCTTATATTCTTATAATTTTAAATGAGGGCACAGTGAAATGAAAATTTTATACTCTATGTTTCTGTTTATTTTTAA
 241 ATCCTTAACAGCAAAATATTTGCCTTTAATTTCTTTTTTATATATACTCTCAGAGAATTCCTCTTAATTTTTAAAGATGC
 321 TGGTGATAATAAAATTCATTAGAAAATTTCCTCATTGTGGAATGAGCATTCTCTTGTTTTAATGTTGGTGTCAGAAAATA
 401 AATATGAAACATTAAGTCCAAAAAAAAAA

ID	Duplex structure	Position	Score	MFE
1	miRNA 3' ccACAAU---UCGGAACGAGUCUCu 5' | ||| | || ||||||| Target 5' ttTTTTATATATACT--CTCAGAGa 3'	274 - 296	144.00	-12.00
2	miRNA 3' ccACAAUUCGGAAC--GAGUCUcu 5' | |||| : ||| ||||| Target 5' tgTTTTAA-TGTTGGTGTCAGAaa 3'	375 - 397	105.00	-5.90
3	miRNA 3' ccacaaUUCGGA-----ACGAGUCUCu 5' |||:|| | : ||||| Target 5' aaaagaAAGTCTAATTATATACAGAGa 3'	4 - 30	104.00	-9.82

Mutant ID	Mutant Position	Mutant Source
COSN20896219	14	COSMIC
COSN31503717	51	COSMIC
COSN31559546	66	COSMIC
COSN1529860	317	COSMIC

Mutant ID	Mutant Position	Mutant Source
rs1481781261	6	dbSNP
rs757512344	9	dbSNP
rs550642244	10	dbSNP
rs1325020983	13	dbSNP
rs1040647929	14	dbSNP
rs948427817	15	dbSNP
rs368974359	16	dbSNP
rs1233496720	23	dbSNP
rs572594404	31	dbSNP
rs530509160	36	dbSNP
rs751460272	39	dbSNP
rs375311052	41	dbSNP
rs745772696	41	dbSNP
rs766285430	42	dbSNP
rs762681787	48	dbSNP
rs1221428890	65	dbSNP
rs1298627178	74	dbSNP
rs924485879	78	dbSNP
rs1346446127	83	dbSNP
rs1216891252	96	dbSNP
rs977221319	97	dbSNP
rs1315676289	99	dbSNP
rs554189215	107	dbSNP
rs968525528	109	dbSNP
rs1214871199	110	dbSNP
rs1021575093	113	dbSNP
rs191375138	122	dbSNP
rs541950255	126	dbSNP
rs564467933	127	dbSNP
rs528147642	129	dbSNP
rs1189384776	135	dbSNP
rs954106447	151	dbSNP
rs966852443	156	dbSNP
rs918083677	158	dbSNP
rs187241293	160	dbSNP
rs750856958	170	dbSNP
rs1418060274	176	dbSNP
rs901229636	181	dbSNP
rs1015777044	189	dbSNP
rs866989847	191	dbSNP
rs58380338	194	dbSNP
rs1369649285	214	dbSNP
rs1240179028	221	dbSNP
rs577099374	221	dbSNP
rs1351106958	223	dbSNP
rs1222847153	227	dbSNP
rs1290402950	233	dbSNP
rs1171707980	246	dbSNP
rs1219291724	249	dbSNP
rs149040287	250	dbSNP
rs1428282619	266	dbSNP
rs901714693	270	dbSNP
rs1040222034	279	dbSNP
rs1382239868	280	dbSNP
rs561920499	280	dbSNP
rs1468846665	291	dbSNP
rs1478929779	297	dbSNP
rs1158150255	300	dbSNP
rs1414982245	302	dbSNP
rs1407392832	307	dbSNP
rs543270939	317	dbSNP
rs1163317129	321	dbSNP
rs1394454817	325	dbSNP
rs1448130609	337	dbSNP
rs1247283983	338	dbSNP
rs1180448827	340	dbSNP
rs753551494	341	dbSNP
rs1373998533	343	dbSNP
rs1049808347	347	dbSNP
rs936675945	351	dbSNP
rs1198839764	357	dbSNP
rs1057175428	360	dbSNP
rs1322425980	368	dbSNP
rs112758842	388	dbSNP
rs924381962	390	dbSNP
rs1200437137	417	dbSNP
rs977149307	423	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.