Phylogenetic Tree Analysis Using RNA Secondary Structure

Abstract

Some mutations in an RNA molecule change the secondary structure from the original one. We have defined a new metric among the secondary structures of the mutants of RNA molecules and implemented in a newly developed secondary structures prediction system which uses multiple processors connected by a local area network. This metric shows non-linearity to the number of mutations: in some cases, only a point mutation makes the secondary structure drastically change, while in others, even with more than 10 points mutations, the structure of the mutant strain is almost the same as that of the original one. A phylogenetic tree was constructed with U1 RNAs of 19 species using this system.