Selected article for: "base pair and structure prediction"
Author: Seemann, Stefan E.; Gorodkin, Jan; Backofen, Rolf
Title: Unifying evolutionary and thermodynamic information for RNA folding of multiple alignments
  • Document date: 2008_10_4
    • ID: wtvfow2f_43
    Snippet: The parameter tuning of PETfold showed that in many cases the quality improves by adding thermodynamic probabilities even when there are highly conserved substructures. PETfold produces the highest MCCs when single-stranded positions are not considered as part of the reliably conserved substructure rel . Furthermore, defining rel which consists of evolutionarily conserved base pairs with high reliability resulted only in a minor improvement. This.....
    Document: The parameter tuning of PETfold showed that in many cases the quality improves by adding thermodynamic probabilities even when there are highly conserved substructures. PETfold produces the highest MCCs when single-stranded positions are not considered as part of the reliably conserved substructure rel . Furthermore, defining rel which consists of evolutionarily conserved base pairs with high reliability resulted only in a minor improvement. This emphasizes that phylogenetic structure information is mostly supported by folding energy. Another unexpected result was the poor weighting of single stranded against base pair positions ( = 0.2), i.e. base pair probabilities have a larger impact on RNA structure prediction.

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