RCAS Motif Discovery

Question

[b.verhagen]

Hi all,

I am trying to discover whether certain RNA molecules contain a motif. I am currently using the RCAS Package in R.

Although, I do not have a problem with identifying motifs in the coding sequence, I, so far, have not been able to unravel any sequence motifs in the UTRs. When running runMotifRG I simply obtain an empty list.

I was wondering whether other people have also experienced this problem, and what the cause could be? Could it be the relatively low amount of UTR-sequences that I have available?

Thanks in advance,

Bram Verhagen