Sequence comparison and secondary structure analysis of the 3′ noncoding region of flavivirus genomes reveals multiple pseudoknots

RNA

Volumn 7, Issue 10, 2001, Pages 1370-1377

  Olsthoorn, René C L ^a   Bol, John F ^a  

^a LEIDEN UNIVERSITY   (Netherlands)

Author keywords

Dengue virus; Japanese encephalitis virus; Mosquito borne flavivirus; Phylogenetic comparison; RNA secondary structure; Tick borne encephalitis; Yellow fever virus

Indexed keywords

VIRUS RNA;

ARTICLE; DENGUE VIRUS; FLAVIVIRUS; JAPANESE ENCEPHALITIS VIRUS; NONHUMAN; NUCLEOTIDE SEQUENCE; PHYLOGENY; PRIORITY JOURNAL; RNA SEQUENCE; RNA STRUCTURE; SEQUENCE ANALYSIS; STRUCTURE ANALYSIS; TICK BORNE ENCEPHALITIS; UNINDEXED SEQUENCE; VIRUS GENOME; YELLOW FEVER FLAVIVIRUS;

BASE SEQUENCE; FLAVIVIRUS; GENOME, VIRAL; MOLECULAR SEQUENCE DATA; NUCLEIC ACID CONFORMATION; RNA, VIRAL; SEQUENCE HOMOLOGY, NUCLEIC ACID; SPECIES SPECIFICITY;

ACARI; DENGUE VIRUS; DHORI VIRUS; FLAVIVIRUS; JAPANESE ENCEPHALITIS VIRUS; MOSQUITO-BORNE VIRUSES; RNA VIRUSES; YELLOW FEVER VIRUS;

EID: 0034763025     PISSN: 13558382     EISSN: None     Source Type: Journal    
DOI: None     Document Type: Article

References (22)

1. Secondary structure model for the last two domains of single-stranded RNA phage Qβ
2. Translation elongation factor-1 alpha interacts with the 3′ stem-loop region of West Nile virus genomic RNA
3. Antigenic relationships between flaviviruses as determined by cross-neutralization tests with polyclonal antisera
4. Evidence that the N-terminal domain of nonstructural protein NS3 from yellow fever virus is a serine protease responsible for site-specific cleavages in the viral polyprotein
5. The computer simulation of RNA folding pathways using a genetic algorithm
6. An approximation of loop free energy values of RNA H-pseudoknots
7. Conserved elements in the 3′ untranslated region of flavivirus RNAs and potential cyclization sequences
8. RNA secondary structure prediction based on free energy and phylogenetic analysis
9. Essential role of cyclization sequences in flavivirus RNA replication
10. Contributions of the brome mosaic virus RNA-3 3′-nontranslated region to replication and translation
11. A phylogenetcally conserved sequence within viral 3′ untranslated RNA pseudoknots regulates translation
12. Sequence of the genes encoding the structural proteins of the low-virulence tick-borne flaviviruses Langat TP21 and Yelantsev
13. Flaviviruses
14. The spatial folding of the 3′ non-coding region of aminoacylatable plant viral RNAs
15. Secondary structure of the 3′ untranslated region of flaviviruses: Similarities and differences
16. Secondary structure of the 3′ noncoding region of flavivirus genomes: Comparative analysis of base pairing probabilities
17. Genetic variation in the 3′ non-coding region of dengue viruses
18. The flavivirus 3′-noncoding region: Extensive size heterogeneity independent of evolutionary relationships among strains of tick-borne encephalitis virus
19. A novel in vitro replication system for Dengue virus
20. On finding all suboptimal foldings of an RNA molecule