RNAcontext is a motif-finding algorithm to infer binding preferences of RNA binding proteins (RBP) from experimental affinity data. The input to RNAcontext consists of a set of sequences together with their associated structure annotation profiles (estimated using SFOLD) and RNA-binding affinity estimates for the given RBP. By learning a motif model that predicts the input affinities, RNAcontext infers the sequence and RNA secondary structure preferences of the RBP.
RBPmotif web server implements the RNAcontext algorithm and an additional analysis framework so that binding preferences of an RBP of interest can be identified from experimental data.
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Nucleic Acids Res. 2013 Jul;41(Web Server issue):W180-6. doi: 10.1093/nar/gkt463. Epub 2013 Jun 10.
RBPmotif: a web server for the discovery of sequence and structure preferences of RNA-binding proteins.
Kazan H1, Morris Q.
H Kazan , D Ray, E Chan, TR Hughes, Q Morris (2010)
RNAcontext: a new method for learning the sequence and structure binding preferences.
PLoS Comput Biol 6(7): e1000832. doi:10.1371/journal.pcbi.1000832