|Title:||Conservation of transient secondary structures in related RNA sequences|
CIHR/MSFHR bioinformatics training program, University of British Columbia
The folding of many classes of RNA molecules into their stable functional conformations takes place co-transcriptionally and may involve the formation of transient secondary structures. However, the identification of such transient structures is experimentally challenging, and these structures are generally ignored in RNA secondary structure prediction. I present a method for identifying evolutionarily conserved RNA helices which conflict the known structure for a group of related sequences.