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_42
Snippet: As shown in Figure 1 , PETfold with = 0.2 and p threshold ss ¼ 1 predicts the best RNA structure as compared to the Rfam annotated structure. These settings optimize the structure of 30 RNA families. The total rejection of the reliably conserved substructure rel (p threshold ss ¼ p threshold bp ¼ 1) or p threshold bp < 0:9 slightly decreases the performance of PETfold. Therefore, we are pragmatic and use p threshold bp ¼ 0:9, which predicts t.....
Document: As shown in Figure 1 , PETfold with = 0.2 and p threshold ss ¼ 1 predicts the best RNA structure as compared to the Rfam annotated structure. These settings optimize the structure of 30 RNA families. The total rejection of the reliably conserved substructure rel (p threshold ss ¼ p threshold bp ¼ 1) or p threshold bp < 0:9 slightly decreases the performance of PETfold. Therefore, we are pragmatic and use p threshold bp ¼ 0:9, which predicts the best RNA structure for 38 families. In summary, we choose = 0.2, = 1, p threshold ss ¼ 1 and p threshold bp ¼ 0:9 as default parameters for PETfold having optimized the structures of 25 RNA families that comprise 54% of the data set.
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