INFO-RNA---a fast approach to inverse RNA folding
Bioinformatics
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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Probabilistic grammatical formalisms such as hidden Markov models (HMMs) and stochastic context-free grammars (SCFGs) have been extensively studied and widely applied in a number of fields. Here, we introduce a new algorithmic problem on HMMs and SCFGs that arises naturally from protein and RNA design, and which has not been previously studied. The problem can be viewed as an inverse to the one solved by the Viterbi algorithm on HMMs or by the CKY algorithm on SCFGs. We study this problem theoretically and obtain the first algorithmic results. We prove that the problem is NP-complete, even for a 3-letter emission alphabet, via a reduction from 3-SAT, a result that has implications for the hardness of RNA secondary structure design. We then develop a number of approaches for making the problem tractable. In particular, for HMMs we develop a branch-and-bound algorithm, which can be shown to have fixed-parameter tractable worst-case running time, exponential in the number of states of the HMM but linear in the length of the structure. We also show how to cast the problem as a Mixed Integer Linear Program.