Author: Gao, James ZM; Li, Linda YM; Reidys, Christian M
Title: Inverse folding of RNA pseudoknot structures Document date: 2010_6_23
ID: 1lojd0xa_49
Snippet: The inverse folding algorithm Inv is based on the ab initio folding algorithm Cross. The input of Inv is the target structure, T. The latter is expressed as a character In Algorithm 7.1, we present the pseudocodes of algorithm Inv. After validation of the target structure (lines 2 to 5 in Algorithm 7.1), similar to INFO-RNA, Inv constructs an initial sequence and then proceeds by a stochastic local search based on the loop decomposition of the ta.....
Document: The inverse folding algorithm Inv is based on the ab initio folding algorithm Cross. The input of Inv is the target structure, T. The latter is expressed as a character In Algorithm 7.1, we present the pseudocodes of algorithm Inv. After validation of the target structure (lines 2 to 5 in Algorithm 7.1), similar to INFO-RNA, Inv constructs an initial sequence and then proceeds by a stochastic local search based on the loop decomposition of the target. This sequence is derived via the routine ADJUST-SEQ. We then decompose the target structure into loops and endow these with a linear order. According to this order we use the routine LOCAL-SEARCH in order to find for each loop a "proper" local solution.
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