title: Multiple alignment and hierarchical clustering of conserved amino acid sequences in the replication-associated proteins of plant RNA viruses.
abstract: We have used multiple alignment computer programs to align and hierarchically cluster the conserved amino acid "signature" sequences found in the replication-associated proteins of all plant RNA viruses sequenced so far. These regions, called "polymerase", "nucleotide-binding" and "N-terminal" are well conserved even between viruses which are only distantly related, and are thus very well suited for this type of analysis. Our results show that the clusterings obtained using these very short amino acid sequences are very robust to computing parameters and are surprisingly well matched with the taxonomic grouping of RNA plant viruses. The possibility of using this system as a new taxonomic criterion is discussed.
authors.affiliation: Station de Pathologie Végétale, Centre de Recherches de Bordeaux, INRA, Villenave d'Ornon Cedex, France.
authors.forename: T
authors.initials: T
authors.lastname: Candresse
authors.forename: M D
authors.initials: MD
authors.lastname: Morch
authors.forename: J
authors.initials: J
authors.lastname: Dunez
mesh_terms: D000595:Amino Acid Sequence; D001665:Binding Sites; D012321:DNA-Directed RNA Polymerases / Q000378:metabolism; D008969:Molecular Sequence Data; D010942:Plant Viruses / Q000145:classification / Q000502:physiology; D012328:RNA Viruses / Q000145:classification / Q000502:physiology; D012689:Sequence Homology, Nucleic Acid; D014764:Viral Proteins / Q000378:metabolism; D014779:Virus Replication
chemical_list: D014764:Viral Proteins; D012321:DNA-Directed RNA Polymerases