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BACKGROUND
Secondary structure forms an important intermediate level of description of nucleic acids that encapsulates the dominating part of the folding energy, is often well conserved in evolution, and is routinely used as a basis to explain experimental findings. Based on carefully measured thermodynamic parameters, exact dynamic programming algorithms… (More)

MOTIVATION
RNA secondary structure contains many non-canonical base pairs of different pair families. Successful prediction of these structural features leads to improved secondary structures with applications in tertiary structure prediction and simultaneous folding and alignment.
RESULTS
We present a theoretical model capturing both RNA pair families… (More)

Chinese hamster ovary (CHO) cells are the predominant cell factory for the production of recombinant therapeutic proteins. Nevertheless, the lack in publicly available sequence information is severely limiting advances in CHO cell biology, including the exploration of microRNAs (miRNA) as tools for CHO cell characterization and engineering. In an effort to… (More)

G-quadruplexes are abundant locally stable structural elements in nucleic acids. The combinatorial theory of RNA structures and the dynamic programming algorithms for RNA secondary structure prediction are extended here to incorporate G-quadruplexes using a simple but plausible energy model. With preliminary energy parameters, we find that the overwhelming… (More)

Stochastic models, such as hidden Markov models or stochastic context-free grammars (SCFGs) can fail to return the correct, maximum likelihood solution in the case of semantic ambiguity. This problem arises when the algorithm implementing the model inspects the same solution in different guises. It is a difficult problem in the sense that proving semantic… (More)

We present a framework of dynamic programming combinators that provides a high-level environment to describe the recursions typical of dynamic programming over sequence data in a style very similar to algebraic dynamic programming (ADP). Using a combination of type-level programming and stream fusion leads to a substantial increase in performance, without… (More)

We develop a theory of algebraic operations over linear and context-free grammars that makes it possible to combine simple "atomic" grammars operating on single sequences into complex, multi-dimensional grammars. We demonstrate the utility of this framework by constructing the search spaces of complex alignment problems on multiple input sequences… (More)

We develop a theory of algebraic operations over linear grammars that makes it possible to combine simple " atomic " grammars operating on single sequences into complex, multi-dimensional grammars. We demonstrate the utility of this framework by constructing the search spaces of complex alignment problems on multiple input sequences explicitly as algebraic… (More)

RNA has become an integral building material in synthetic biology. Dominated by their secondary structures, which can be computed efficiently, RNA molecules are amenable not only to in vitro and in vivo selection, but also to rational, computation-based design. While the inverse folding problem of constructing an RNA sequence with a prescribed ground-state… (More)

MOTIVATION
RNA family models group nucleotide sequences that share a common biological function. These models can be used to find new sequences belonging to the same family. To succeed in this task, a model needs to exhibit high sensitivity as well as high specificity. As model construction is guided by a manual process, a number of problems can occur, such… (More)