Stem Trace: An interactive visual tool for comparative RNA structure analysis

Motivation: Stem Trace is one of the latest tools available in STRUCTURELAB, an RNA structure analysis computer workbench. The paradigm used in STRUCTURELAB views RNA structure determination as a problem of dealing with a database of a large number of computationally generated structures. Stem Trace provides the capability to analyse this data set in a novel, visually driven, interactive and exploratory way In addition to providing graphs at a high level of abstraction, it is also connected with complementary visualization tools which provide orthogonal views of the same data, as well as drawing of structures represented by a stem trace. Thus, on top of being an analysis tool, Stem Trace is a graphical user interface to an RNA structural information database. Results: We illustrate Stem Trace's capabilities with several examples of the analysis of RNA folding data performed rf on 24 strains of HIV-1, HIV-2 and SIV sequences around the HIV dimerization region. This dimer linkage site has been found to play a role in encapsidation, reverse transcription, recombination, and inhibition of translation. Our examples show how Stern Trace elucidates preservation of structures in this region across the various strains of HIV. Availability: The program can be made available upon request. It runs on SUN; SGI and DEC (Compaq) Unix workstations.