Author: Theis, Corinna; Reeder, Jens; Giegerich, Robert
Title: KnotInFrame: prediction of -1 ribosomal frameshift events Document date: 2008_9_27
ID: 4ov0j2u3_20
Snippet: (i) In the search phase, we scan the input sequences for occurrences of the consensus slippery site in the correct reading frame. The downstream region of each slippery site is checked for suitability as a frameshift signal. This is done by comparing the minimal free energy of an enforced pseudo-knotted folding with the MFE of a freely folded structure. The former energy is computed by pknotsRG-fs, the latter by RNAfold. (ii) In the filtering pha.....
Document: (i) In the search phase, we scan the input sequences for occurrences of the consensus slippery site in the correct reading frame. The downstream region of each slippery site is checked for suitability as a frameshift signal. This is done by comparing the minimal free energy of an enforced pseudo-knotted folding with the MFE of a freely folded structure. The former energy is computed by pknotsRG-fs, the latter by RNAfold. (ii) In the filtering phase, three criteria based on the energy values of the free and the constrained folding are applied to reduce the number of candidates.
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