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.

    Search related documents:
    Co phrase search for related documents
    • base pair and pair position: 1, 2, 3, 4, 5, 6
    • base pair and pair probability: 1, 2, 3, 4, 5
    • base pair and parameter tuning: 1, 2, 3
    • base pair and RNA structure prediction: 1, 2, 3
    • base pair and single strand: 1, 2
    • base pair and structure information: 1, 2, 3
    • base pair and structure prediction: 1, 2, 3, 4, 5, 6
    • base pair and substructure rel: 1
    • base pair position and pair position: 1, 2, 3, 4, 5, 6
    • base pair position and parameter tuning: 1
    • base pair position and structure prediction: 1
    • base pair position and substructure rel: 1
    • base pair probability and pair probability: 1, 2, 3, 4, 5
    • energy fold and high reliability: 1
    • energy fold and phylogenetic structure information: 1
    • energy fold and structure information: 1
    • energy fold and structure prediction: 1
    • energy fold and substructure rel: 1