Author: Gao, James ZM; Li, Linda YM; Reidys, Christian M
Title: Inverse folding of RNA pseudoknot structures Document date: 2010_6_23
ID: 1lojd0xa_28
Snippet: INFO-RNA constructs sequences folding into a given secondary structure by employing a dynamic programming method for finding a well suited initial sequence. This sequence has a lowest energy with respect to the T. Since the latter does not necessarily fold into T, (due to potentially existing competing configurations) INFO-RNA then utilizes an improved (relative to the local search routine used in RNAinverse) stochastic local search in order to f.....
Document: INFO-RNA constructs sequences folding into a given secondary structure by employing a dynamic programming method for finding a well suited initial sequence. This sequence has a lowest energy with respect to the T. Since the latter does not necessarily fold into T, (due to potentially existing competing configurations) INFO-RNA then utilizes an improved (relative to the local search routine used in RNAinverse) stochastic local search in order to find a sequence in the neutral network of T. In contrast to RNAinverse, INFO-RNA allows for increasing the distance to the target structure. At the same time, only positions that do not pair correctly and positions adjacent to these are examined.
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