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Presented here is a comprehensive computational survey of evolutionarily conserved secondary structure motifs in the genomic RNAs of the family Flaviviridae: This virus family consists of the three genera Flavivirus, Pestivirus and Hepacivirus and the group of GB virus C/hepatitis G virus with a currently uncertain taxonomic classification. Based on the(More)
The family Picornaviridae contains important pathogens including, for example, hepatitis A virus and foot-and-mouth disease virus. The genome of these viruses is a single messenger-active (+)-RNA of 7200-8500 nt. Besides coding for the viral proteins, it also contains functionally important RNA secondary structures, among them an internal ribosomal entry(More)
A plethora of new functions of non-coding RNAs (ncRNAs) have been discovered in past few years. In fact, RNA is emerging as the central player in cellular regulation, taking on active roles in multiple regulatory layers from transcription, RNA maturation, and RNA modification to translational regulation. Nevertheless, very little is known about the(More)
Most functional RNA molecules have characteristic structures that are highly conserved in evolution. Many of them contain pseudoknots. Here, we present a method for computing the consensus structures including pseudoknots based on alignments of a few sequences. The algorithm combines thermodynamic and covariation information to assign scores to all possible(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)
In bioinformatics there exist research topics that cannot be uniquely characterized by a set of key words because relevant key words are (i) also heavily used in other contexts and (ii) often omitted in relevant documents because the context is clear to the target audience. Information retrieval interfaces such as entrez/Pubmed produce either low precision(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)
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