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Understanding the relationship between protein sequence and structure is one of the great challenges in biology. In the case of the ubiquitous coiled-coil motif, structure and occurrence have been described in extensive detail, but there is a lack of insight into the rules that govern oligomerization, i.e. how many α-helices form a given coiled coil. To(More)
RNA molecules that can fold into two or more predefined alternative metastable structures can be designed rationally. We outline an algorithm for this task that reduces the problem to vertex coloring the union of all prescribed outerplanar secondary structure graphs. Starting from an ear decomposition of this composite graph colorings are produced by a(More)
Within the last years it became clear that RNA molecules do not only store and transfer genetic information but they can also act as catalytic units. On the one hand, RNA was seen once as an 'information-exchanging-unit' between DNA and proteins. On the other hand nowadays it has become evident that RNA fulfills important regulation tasks in living cells,(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)
High quality sequence alignments of RNA and DNA sequences are a prerequisite for the comparative analysis of genomic sequence data. The high level of sequence heterogeneity, as compared to proteins, makes good alignments of nucleic acid sequences often impossible. In many cases, the nucleic acid sequences under consideration, or parts of them, code for(More)
The aim of the work described in this thesis was the creation of a software tool to support the rational design of RNA molecules capable of forming two or more alternative metastable structures. This required the creation of a logical information model, thus isolating relevant aspects of the biological problem as posed, and incorporating these into a(More)
Overview I comment on the question of how to deal appropriately with vague information by formal means. I am critical of attempts to endow vague concepts with semantics in analogy to crisp concepts that refer to a mathematical structure. I argue, to the contrary, that vagueness pertains to the variability of the models associated with a particular mode of(More)