Fig. 1

DCA-scapes provide global models of RNA recognition. RNA-binding proteins are incubated with libraries of in vitro transcribed RNA containing a 20 base random region (scheme adapted from ref. ⁴⁶). RNA–protein complexes are isolated through washing and reverse transcribed to cDNA. Transcription adapters are attached to the library using PCR and the selection process is repeated for five rounds. After selection, the pool is subjected to high-throughput sequencing. The 20-mer region is used as an input for the creation of a global model. The model considers both the local nucleotide propensities and pairwise couplings to calculate a Hamiltonian score. These scores can be used to detect binding sites and predict the outcome of specific mutations. Pairwise interactions are visualized on a landscape and provide hints of molecular interactions relevant for recognition