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Research highlight : AUTOMATED PREDICTION OF THREE-WAY JUNCTION TOPOLOGICAL FAMILIES IN RNA SECONDARY STRUCTURES
AUTOMATED PREDICTION OF THREE-WAY JUNCTION TOPOLOGICAL FAMILIES IN RNA SECONDARY STRUCTURES
11 February 2012

Alexis Lamiable, Dominique Barth, Alain Denise, Franck Quessette, Sandrine Vial, Éric Westhof.
Computational Biology and Chemistry 37 (2012) 1–5
We present an algorithm for automatically predicting the topological family of any RNA three-way junction,
given only the information from the secondary structure: the sequence and the Watson–Crick
pairings. The parameters of the algorithm have been determined on a data set of 33 three-way junctions
whose 3D conformation is known. We applied the algorithm on 53 other junctions and compared
the predictions to the real shape of those junctions. We show that the correct answer is selected out
of nine possible configurations 64% of the time. Additionally, these results are noticeably improved if
homology information is used. The resulting software, Cartaj, is available online and downloadable (with
source) at: http://cartaj.lri.fr.



Keyword
  ° Bioinformatics

Group
  ° Algorithms and Complexity
  ° Bioinformatics

Contact
  ° DENISE Alain
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