Work on nucleic acid structure has continued in a variety of collaborations and directions. The RNA secondary structure analysis system has expanded to include more functionality for analyzing RNA conformations from various perspectives. This has involved the development of new algorithms to explore secondary structure motifs and RNA tertiary structure. This has made available an experimental computer workbench to allow a researcher to interactively pursue various areas of interest concerning RNA 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 permits queries of relationships that exist in the RNA secondary structure problem domain involving various software/hardware complexes available at the FCRF. The system is currently being ported to a SUN workstation thus allowing broader access. Algorithms have been developed that involve RNA secondary structure analysis specifically the measurement and visualization of structural similarity from global and contextual viewpoints. A very fast algorithm has been developed to compare RNA structures using the concept of levels of abstraction. This permits the definition and searching of structures from loose to a more restricted specifications. A research effort has also begun using the system examining the potential effects of tertiary RNA interactions such as loop-loop bindings. The system and new algorithms have been used to study the Lll operon of E. coli with respect to regulation effects of the Ll protein. Also, the structural effects of the translation efficiency of the lamb gene of E. coli was studied. Work has begun using the structure analysis system to study the structural aspects of polio. Initial observations indicate that secondary and possibly tertiary structural components may correlate with ribosomal binding sites.
