I need to scan mRNAs for binding motifs of RBPs (RNA binding proteins) in human.
After some research I came across this tutorial on how to find candidate binding sites of known transcription factors. So far I did not saw an implemented tool to directly work with RNA or RBPs.
I downloaded a file from CISBP-RNA containing information on some RNA binding proteins. The PWMs can be downloaded as txt files. I use Gencode GRCh37.p13.
Now I want to search for potential binding sites per transcript and per 3'UTR (in RNA code). What is the most efficient way to procede? I downloaded all UTR et c. sequences using biomaRt, but it contains just the DNA sequences. I transcribed the sequence into RNA already manually, but then I can't use the matchPWM function anymore (it just works for DNAString objects).
Is there also an matchPWM function for RNA sequences that is able to handle U instead of T? matchPWM is just able to handle DNA sequences.
Thanks for help in advance!