Bioinformatics, Vol 15, 16-31, Copyright © 1999 by Oxford University Press
W Kasprzak and B Shapiro
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.
ARTICLES
Stem Trace: an interactive visual tool for comparative RNA structure analysis
Intramural Research Support Program, SAIC Frederick, National Cancer Institute/FCRDC, Bldg 469, Rm 150C, MD 21702, USA. kasprzak@ncifcrf.gov
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