TY - JOUR
AU - Shapiro, B
AB - 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 analyze this data set in a novel, visually driven, interactive and exploratory way. In addition to providing graphs at a high level of ion, 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 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 Stem 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.
TI - Stem Trace: an interactive visual tool for comparative RNA structure analysis.
JF - Bioinformatics
DO - 10.1093/bioinformatics/15.1.16
DA - 1999-01-01
UR - https://www.deepdyve.com/lp/oxford-university-press/stem-trace-an-interactive-visual-tool-for-comparative-rna-structure-5yP6CSRoLK
SP - 16
EP - 31
VL - 15
IS - 1
DP - DeepDyve
ER -