Author: Gao, James ZM; Li, Linda YM; Reidys, Christian M
Title: Inverse folding of RNA pseudoknot structures Document date: 2010_6_23
ID: 1lojd0xa_26
Snippet: RNAinverse is the first inverse-folding algorithm that derives sequences that realize given RNA secondary structures as mfe-configuration. In its initialization step, a random compatible sequence s for the target T is generated. Then RNAinverse proceeds by updating the sequence s to s′, s′′ ... step by step, minimizing the structure distance between the mfe structure of s′ and the target structure T. Based on the observation, that the ene.....
Document: RNAinverse is the first inverse-folding algorithm that derives sequences that realize given RNA secondary structures as mfe-configuration. In its initialization step, a random compatible sequence s for the target T is generated. Then RNAinverse proceeds by updating the sequence s to s′, s′′ ... step by step, minimizing the structure distance between the mfe structure of s′ and the target structure T. Based on the observation, that the energy of a substructure contributes additively to the mfe of the molecule, RNAinverse optimizes "small" substructures first, eventually extending these to the entire structure. While optimizing substructures, RNAinverse does an adaptive walk in order to decrease the structure distance. In fact, this walk is based entirely on random compatible mutations.
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