Hi,

I downloaded binding motifs of multiple RBPs (RNA binding proteins) on CISBP-RNA and want to search on which sequences they bind. I downloaded the sequences from biomaRt, an R library. There is a function, matchPWM, which works with DNA sequences, but not for RNA sequences. Apparently it does not find reverse complementary sequences, so I might change the U into a T, however, I think this is not good practise. (Also the seqLogo function for plotting binding motifs does not work for RNA sequences, however, I found a walkaround via ghostscript to plot those. But I guess it is very complicated and I don't understand why the function can handle DNAStrings but not RNAString objects.)

Is there another tool, R library... you recommend for this purpose?

Thanks for your suggestions!