RNAspa: a shortest path approach for comparative prediction of the secondary structure of ncRNA molecules

Background: In recent years, RNA molecules that are not translated into proteins (ncRNAs) have drawn a great deal of attention, as they were shown to be involved in many cellular functions. One of the most important computational problems regarding ncRNA is to predict the secondary structure of a molecule from its sequence. In particular, we attempted to predict the secondary structure for a set of unaligned ncRNA molecules that are taken from the same family, and thus presumably have a similar structure. Results: We developed the RNAspa program, which comparatively predicts the secondary structure for a set of ncRNA molecules in linear time in the number of molecules. We observed that in a list of several hundred suboptimal minimal free energy (MFE) predictions, as provided by the RNAsubopt program of the Vienna package, it is likely that at least one suggested structure would be similar to the true, correct one. The suboptimal solutions of each molecule are represented as a layer of...

• Type: Journal
• Year: 2007
• Where: BMCBI
• Authors: Yair Horesh, Tirza Doniger, Shulamit Michaeli, Ron Unger
• Keywords: BMCBI 2007, Molecules, RNA Molecules, Secondary Structures