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_32
Snippet: Gaps are treated in a two-step procedure. First, all columns are removed from the alignment where 75% of the sequences have nucleotides. These columns are integrated as gaps in the consensus secondary structure at the end, a strategy that is adapted from Pfold. Second, sequencedependent probabilities p s u k;l and q s u k are calculated without gaps and probabilities of gaps are estimated as the average in the appropriate column of the alignment......
Document: Gaps are treated in a two-step procedure. First, all columns are removed from the alignment where 75% of the sequences have nucleotides. These columns are integrated as gaps in the consensus secondary structure at the end, a strategy that is adapted from Pfold. Second, sequencedependent probabilities p s u k;l and q s u k are calculated without gaps and probabilities of gaps are estimated as the average in the appropriate column of the alignment.
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