Work on nucleic acid structure has continued in a variety of collaborations and directions. Among these include the development of a fully integrated computer environment for the analysis of RNA secondary structure. The others have involved the development of new algorithms to help analyze these structures. One of the objects of this research is to make available an experimental computer workbench to allow a researcher to interactively pursue various areas of interest concerning RNA secondary structure in a coherent way. This includes both the use of facilities to explore in detail multiple structures as well as individual RNA structures. This system is forming the basis for an expert system which is permitting intelligent queries of relationships that exist in the RNA secondary structure problem domain involving various software/hardware complexes available at the Frederick Cancer Research Facility. Several algorithms have been developed that involve RNA secondary structure analysis. These include several algorithms to measure structural similarity, an algorithm to determine how RNA structural energies are related to sequence composition and an algorithm to determine structural consensus. Work has begun on a new algorithm for speeding up the prediction of RNA secondary structure by jumping over portions of structure that are not going to add very much to a given structure. Also, a new algorithm for secondary structure comparison based on precise tree matching is being developed. The DNA structure analysis program which was enhanced to include rules on DNA melting was used to analyze procaryotic promoter regions. Using this system we were able to show that promoter regions appear to be related to the stabilizing energies of the promoter.
