Computational protocol: Finding RNA structure in the unstructured RBPome

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Protocol publication

[…] We explored the overall statistic of structural binding preferences amongst the set of RNA-binding proteins in the RNAcompete dataset []. We used the set of learned models from the RCK website []. We identified for each protein the k-mer w and structural context a with the highest binding score. We calculated the binding scores for k-mer w in the other structural contexts. The relative weight of those scores are the structural preferences assigned to that protein. For Fig. we calculated the log of the ratio of paired to unpaired scores. For Fig. we calculated the log of the ratio of loop to external scores. […]

Pipeline specifications

Software tools RNAcompete, RCK
Application CLIP-seq analysis
Chemicals Amino Acids