Inverting the Viterbi algorithm: an abstract framework for structure design
Proceedings of the 25th international conference on Machine learning
rnaDesign: local search for RNA secondary structure design
CIBCB'09 Proceedings of the 6th Annual IEEE conference on Computational Intelligence in Bioinformatics and Computational Biology
Performance prediction for RNA design using parametric and non-parametric regression models
CIBCB'09 Proceedings of the 6th Annual IEEE conference on Computational Intelligence in Bioinformatics and Computational Biology
Flexible RNA design under structure and sequence constraints using formal languages
Proceedings of the International Conference on Bioinformatics, Computational Biology and Biomedical Informatics
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Motivation: The structure of RNA molecules is often crucial for their function. Therefore, secondary structure prediction has gained much interest. Here, we consider the inverse RNA folding problem, which means designing RNA sequences that fold into a given structure. Results: We introduce a new algorithm for the inverse folding problem (INFO-RNA) that consists of two parts; a dynamic programming method for good initial sequences and a following improved stochastic local search that uses an effective neighbor selection method. During the initialization, we design a sequence that among all sequences adopts the given structure with the lowest possible energy. For the selection of neighbors during the search, we use a kind of look-ahead of one selection step applying an additional energy-based criterion. Afterwards, the pre-ordered neighbors are tested using the actual optimization criterion of minimizing the structure distance between the target structure and the mfe structure of the considered neighbor. We compared our algorithm to RNAinverse and RNA-SSD for artificial and biological test sets. Using INFO-RNA, we performed better than RNAinverse and in most cases, we gained better results than RNA-SSD, the probably best inverse RNA folding tool on the market. Availability: www.bioinf.uni-freiburg.de?Subpages/software.html Contact: backofen@informatik.uni-freiburg.de Supplementary information: Supplementary data are available on Bioinformatics online.