Detection of non-coding RNAs on the basis of predicted secondary structure formation free energy change

Background: Non-coding RNAs (ncRNAs) have a multitude of roles in the cell, many of which remain to be discovered. However, it is difficult to detect novel ncRNAs in biochemical screens. To advance biological knowledge, computational methods that can accurately detect ncRNAs in sequenced genomes are therefore desirable. The increasing number of genomic sequences provides a rich dataset for computational comparative sequence analysis and detection of novel ncRNAs. Results: Here, Dynalign, a program for predicting secondary structures common to two RNA sequences on the basis of minimizing folding free energy change, is utilized as a computational ncRNA detection tool. The Dynalign-computed optimal total free energy change, which scores the structural alignment and the free energy change of folding into a common structure for two RNA sequences, is shown to be an effective measure for distinguishing ncRNA from randomized sequences. To make the classification as a ncRNA, the total free ene...

• Type: Journal
• Year: 2006
• Where: BMCBI
• Authors: Andrew V. Uzilov, Joshua M. Keegan, David H. Mathews
• Keywords: BMCBI 2006, Free Energy Changes, Sequence Pair, Support Vector Machine