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_20
Snippet: The basic idea of MEA scoring is to consider Pr(r(), A) as a probability distribution over consensus structures, where higher probabilities denote a better fit to the alignment and its associated evolutionary history. We write position i 6 2 as short for 'position i is not involved in a base pair in ' [i.e. 8j : ði; jÞ 6 2 ^ðj; iÞ 6 2 ð Þ ]. Given the structure and an alignment A with m columns, the set of all unpaired positions in the cons.....
Document: The basic idea of MEA scoring is to consider Pr(r(), A) as a probability distribution over consensus structures, where higher probabilities denote a better fit to the alignment and its associated evolutionary history. We write position i 6 2 as short for 'position i is not involved in a base pair in ' [i.e. 8j : ði; jÞ 6 2 ^ðj; iÞ 6 2 ð Þ ]. Given the structure and an alignment A with m columns, the set of all unpaired positions in the consensus structure is denoted as ¼ fi 6 2 j 1 i mg. Then, we can compute the expected overlap ex-over evo () of a specific consensus structure with all possible consensus structures, weighted according to their probabilities. This can be done as follows:
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