Tree graphs of RNA secondary structures and their comparisons.

To facilitate comparison of RNA secondary structures each structure is represented as an ordered labeled tree. Several alternate secondary structures yielding a set of trees can be computed for any given RNA molecule (sequence). Frequently recurring subtrees are searched in this set of trees. The consensus structure motifs are then selected and used to construct a secondary structure model of the RNA. Given the difficulties involved in RNA secondary structure calculations, this procedure may significantly improve our predictive capabilities. In addition, the change of secondary structures between two different RNA sequences is described as a transformation of ordered trees. The transferable ratio of tree A from tree B is defined as a proportion of the largest common subtrees in trees A and B occurring in tree A. The method is applied to the study of the mechanism of human alpha 1 globin pre-mRNA splicing. In the study, two tentative splicing mechanisms, A and B, with different orders of intron excision from alpha 1 globin pre-mRNA have been stimulated. A possible relationship between the structural features of the secondary structures and the order of intron excision in the pathway of precursor splicing of human alpha 1 globin is discussed.