|Subject:||RNA Secondary Structure Prediction|
|Draft:||" RNA secondary structure prediction with a single hot spot "|
RNA secondary structure prediction with a single hot spot
Jihon Ren has developed a heuristic algorithm to predict pseudoknotted secondary structures. The heuristic algorithm identifies hotspots, i.e. low energy stems, and forces them to be unpaired bases when trying to find the optimal, i.e. minimum free energy, secondary structure that contains the hotspot.
A better approach might be: given a set of hotspots, find the minimum free energy secondary structure that contains those hotspots, but would be pseudoknot free if the hotspots were removed.
For now, we assume that there is only one known hotspot in the structure, and only pseudoknotted loops that overlap with the band are possible. We also assume that there are no unpaired bases inside the band [m,m'] union [k',k]. We try to calculated the minimum free energy for such structure.
The outline of this talk is available at http://www.cs.ubc.ca/~szhao/writing.pdf