Author: Theis, Corinna; Reeder, Jens; Giegerich, Robert
Title: KnotInFrame: prediction of -1 ribosomal frameshift events Document date: 2008_9_27
ID: 4ov0j2u3_49
Snippet: The KnotInFrame pipeline can be seen as a model case of developing a thermodynamic matcher, in our case pknotsRG-fs, and embedding it in a pipeline with further search criteria and filters. Development of thermodynamic matchers is supported by the tool Locomotif (30) , which allows to graphically design RNA structures, annotated with sequence information and length restrictions. From such graphics, a thermodynamic matcher is produced automaticall.....
Document: The KnotInFrame pipeline can be seen as a model case of developing a thermodynamic matcher, in our case pknotsRG-fs, and embedding it in a pipeline with further search criteria and filters. Development of thermodynamic matchers is supported by the tool Locomotif (30) , which allows to graphically design RNA structures, annotated with sequence information and length restrictions. From such graphics, a thermodynamic matcher is produced automatically, bypassing tedious low-level programming and debugging. In the course of this work, we have also extended the repertoire of structural building blocks in Locomotif by a pseudoknot building block. In this way, it will be easy for workers in the field to construct their own pipelines akin to KnotInFrame, for RNA motifs of moderate size, with and without pseudoknots.
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