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PHYLOGENETIC PREDICTION OF CIS-ACTING ELEMENTS: A CRE-LIKE SEQUENCE IN NOROVIRUS GENOME?
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Fundação Oswaldo Cruz. Instituto Oswaldo Cruz. Laboratório de Virologia Comparada e Ambiental. Rio de Janeiro, RJ. Brasil.
Centro de Investigaciones Nucleares. Facultad de Ciencias. Laboratorio de Virología Molecular. Montevideo, Uruguay.
Fundação Oswaldo Cruz. Instituto Oswaldo Cruz. Laboratório de Virologia Comparada e Ambiental. Rio de Janeiro, RJ. Brasil.
Fundação Oswaldo Cruz. Instituto Oswaldo Cruz. Laboratório de Virologia Comparada e Ambiental. Rio de Janeiro, RJ. Brasil.
Centro de Investigaciones Nucleares. Facultad de Ciencias. Laboratorio de Virología Molecular. Montevideo, Uruguay.
Centro de Investigaciones Nucleares. Facultad de Ciencias. Laboratorio de Virología Molecular. Montevideo, Uruguay.
Fundação Oswaldo Cruz. Instituto Oswaldo Cruz. Laboratório de Virologia Comparada e Ambiental. Rio de Janeiro, RJ. Brasil.
Fundação Oswaldo Cruz. Instituto Oswaldo Cruz. Laboratório de Virologia Comparada e Ambiental. Rio de Janeiro, RJ. Brasil.
Centro de Investigaciones Nucleares. Facultad de Ciencias. Laboratorio de Virología Molecular. Montevideo, Uruguay.
Abstract
Discrete RNA structures such as cis-acting replication elements (cre) in the coding region of RNA virus genomes create characteristic suppression of synonymous site variability (SSSV). Different phylogenetic methods have been developed to predict secondary structures in RNA viruses, for high-resolution thermodynamic scanning and for detecting SSSV. These approaches have been successfully in predicting cis-acting signals in different members of the family Picornaviridae and Caliciviridae. In order to gain insight into the identification of cis-acting signals in viruses whose mechanisms of replication are currently unknown, we performed a phylogenetic analysis of complete genome sequences from 49 Human Norovirus (NoV) strains.
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