Nucleic Acids Research, Vol 25, Issue 17 3514-3522, Copyright © 1997 by Oxford University Press
F Chetouani, P Monestie, P Thebault, C Gaspin and B Michot
With ESSA, we propose an approach of RNA secondary structure analysis based
on extensive viewing within a friendly graphical interface. This computer
program is organized around the display of folding models produced by two
complementary methods suitable to draw long RNA molecules. Any feature of
interest can be managed directly on the display and highlighted by a rich
combination of colours and symbols with emphasis given to structural probe
accessibilities. ESSA also includes a word searching procedure allowing
easy visual identification of structural features even complex and
degenerated. Analysis functions make it possible to calculate the
thermodynamic stability of any part of a folding using several models and
compare homologous aligned RNA both in primary and secondary structure. The
predictive capacities of ESSA which brings together the experimental,
thermodynamic and comparative methods, are increased by coupling it with a
program dedicated to RNA folding prediction based on constraints management
and propagation. The potentialities of ESSA are illustrated by the
identification of a possible tertiary motif in the LSU rRNA and the
visualization of a pseudoknot in S15 mRNA.
ARTICLES
ESSA: an integrated and interactive computer tool for analysing RNA secondary structure
Laboratoire de Biologie Moleculaire Eucaryote du C.N.R.S., Universite Paul Sabatier, 118 route de Narbonne, 31062 Toulouse Cedex, France.
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