I have a couple PWMs for RNA binding proteins and I also have the sequences of candidate UTRs in different groups as a DNAStringSet. I'd like to see how many of the UTRs (and which ones) in each group match a given PWM. However, it looks like the matchPWM function in Biostrings only supports a single sequence rather than a DNAStringSet. Is there a way to do this besides sticking all of my sequences together, matching, breaking them apart or looping through each sequence?

Thanks

I'm pretty sure you can use sapply for this, something along the lines of:  

sapply(my_DNAStringSet, FUN = matchPWM, pwm = my_PWM)

That works, but is incredibly slow once I start looping through all of my UTRs and even a few RNA binding proteins. Is there another bioconductor package or program outside that would be significantly faster?