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_59
Snippet: A second possible improvement considers the fact that structural stability is at least partially accounted twice since Pfold already favors stable base pairs such as G-C. This does not pose a major problem since the thermodynamic part adds a lot of new information like sequence-dependent stacking or properties of the complete structure ensemble (encoded in base pair probabilities). Nevertheless, it would be nice to explicitly separate these diffe.....
Document: A second possible improvement considers the fact that structural stability is at least partially accounted twice since Pfold already favors stable base pairs such as G-C. This does not pose a major problem since the thermodynamic part adds a lot of new information like sequence-dependent stacking or properties of the complete structure ensemble (encoded in base pair probabilities). Nevertheless, it would be nice to explicitly separate these different information sources in a future version.
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