Author: Theis, Corinna; Reeder, Jens; Giegerich, Robert
Title: KnotInFrame: prediction of -1 ribosomal frameshift events Document date: 2008_9_27
ID: 4ov0j2u3_8
Snippet: This is the work we build upon. Despite its overall good architecture, there is one shortcoming in the procedure. Sequences are forced to fold into a pseudoknot in the first step but are folded freely in the second step. Thus, the result of the procedure is indeed 2-fold: (i) the final candidates have the theoretical potential to fold a pseudoknot, and (ii) they have a MFE folding which is more stable than expected by random. However, it is not g.....
Document: This is the work we build upon. Despite its overall good architecture, there is one shortcoming in the procedure. Sequences are forced to fold into a pseudoknot in the first step but are folded freely in the second step. Thus, the result of the procedure is indeed 2-fold: (i) the final candidates have the theoretical potential to fold a pseudoknot, and (ii) they have a MFE folding which is more stable than expected by random. However, it is not guaranteed that the stable structure which causes the good z-score actually is a pseudoknot. In fact, we found that from 1679 strong candidates only 163 contain a pseudoknot. The pseudoknot, which was folded by RNAmotif in step one, may have an energy similar to the MFE folding, but more likely, it will be less stable and hence, less probable to be formed in equilibrium.
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