Author: Theis, Corinna; Reeder, Jens; Giegerich, Robert
Title: KnotInFrame: prediction of -1 ribosomal frameshift events Document date: 2008_9_27
ID: 4ov0j2u3_16
Snippet: In this way, we obtain a specialized RNA-folding program pknotsRG-fs, which computes for a given input sequence the minimal free energy À1 PRF pseudoknot. Such a program has been called a thermodynamic matcher (TDM) in (18) . If a sequence cannot form a pseudoknot with negative energy, the open structure is returned (with energy equal to zero). The compiled code takes less than a second to fold a sequence of length 100. The complete grammar is a.....
Document: In this way, we obtain a specialized RNA-folding program pknotsRG-fs, which computes for a given input sequence the minimal free energy À1 PRF pseudoknot. Such a program has been called a thermodynamic matcher (TDM) in (18) . If a sequence cannot form a pseudoknot with negative energy, the open structure is returned (with energy equal to zero). The compiled code takes less than a second to fold a sequence of length 100. The complete grammar is available at the project website. Readers with alternative ideas about the structure of the À1 PRF signal can use it as a starting point for a faithful implementation of a corresponding TDM.
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