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Comparative Study
. 1997 Jul;3(7):779-91.

Secondary structure of the 3'-noncoding region of flavivirus genomes: comparative analysis of base pairing probabilities

S Rauscher  1 , C Flamm, C W Mandl, F X Heinz, P F Stadler
Affiliations
Comparative Study

Secondary structure of the 3'-noncoding region of flavivirus genomes: comparative analysis of base pairing probabilities

S Rauscher et al. RNA. 1997 Jul.

Abstract

The prediction of the complete matrix of base pairing probabilities was applied to the 3' noncoding region (NCR) of flavivirus genomes. This approach identifies not only well-defined secondary structure elements, but also regions of high structural flexibility. Flaviviruses, many of which are important human pathogens, have a common genomic organization, but exhibit a significant degree of RNA sequence diversity in the functionally important 3'-NCR. We demonstrate the presence of secondary structures shared by all flaviviruses, as well as structural features that are characteristic for groups of viruses within the genus reflecting the established classification scheme. The significance of most of the predicted structures is corroborated by compensatory mutations. The availability of infectious clones for several flaviviruses will allow the assessment of these structural elements in processes of the viral life cycle, such as replication and assembly.

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