RNAcompete / RNAcompete-S
RNAcompete is a method for the systematic analysis of RNA binding specificities that uses a single binding reaction to determine the relative preferences of RBPs for short RNAs that contain a complete range of k-mers in structured and unstructured RNA contexts.
RNAcompete-S couples a single-step competitive binding reaction with an excess of random RNA 40-mers to a custom computational pipeline for interrogation of the bound RNA sequences and derivation of SSMs (Sequence and Structure Models).
rnascan is a (mostly) Python suite to scan RNA sequences and secondary structures with sequence and secondary structure PFMs. Secondary structure is represented as weights in different secondary structure contexts, similar to how a PFM represents weights of different nucleotides or amino acids.
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Nat Biotechnol. 2009 Jul;27(7):667-70. doi: 10.1038/nbt.1550. Epub 2009 Jun 28.
Rapid and systematic analysis of the RNA recognition specificities of RNA-binding proteins.
Ray D, Kazan H, Chan ET, Peña Castillo L, Chaudhry S, Talukder S, Blencowe BJ, Morris Q, Hughes TR.
Cook, K.B., Vembu, S., Ha, K.C.H., Zheng, H., Laverty, K.U., Hughes, T.R., Ray, D., Morris, Q.D., 2017.
RNAcompete-S: Combined RNA sequence/structure preferences for RNA binding proteins derived from a single-step in vitro selection.
Methods 126, 18–28.