A computational procedure for assessing the significance of RNA secondary structure

In our recent series of papers, we have used the structuresof statistical significance from Monte Carlo simulations toimprove the predictions of secondary structure of RNA and toanalyze the possible role of locally significant structuresin the ljfe cycle of human immunodeficiency virus. Because ofintensive computational requirements for Monte Carlo simulation,it becomes impractical even using a supercomputer to assessthe significance of a structure with a window size > 200along an RNA sequence of 1000 bases or more. In this paper,we have developed a new procedure that drastically reduces thetime needed to assess the significance of structures. In fact,the efficiency of this new method allows us to assess structureson the VAX as well as the CRAY Received on May 11, 1989; accepted on August 22, 1989