CIMS is a computational method to analyze HITS-CLIP data for determining the exact protein-RNA crosslink sites and thereby mapping protein-RNA interactions at the single-nucleotide resolution. This method is based on the observation that UV cross linked amino-acid-RNA adduct introduce reverse transcription errors in cDNAs at certain frequencies, which are captured by sequencing and comparison of CLIP tags with the reference genome.
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Nat Biotechnol. 2011 Jun 1;29(7):607-14. doi: 10.1038/nbt.1873.
Mapping in vivo protein-RNA interactions at single-nucleotide resolution from HITS-CLIP data.
Zhang C, Darnell RB.