Topological organization of picornaviral genomes: Statistical prediction of RNA structural signals

Seminars in Virology

Volumn 8, Issue 3, 1997, Pages 231-241

  Palmenberg, Ann C ^a   Sgro, Jean Yves ^a  

^a UNIVERSITY OF WISCONSIN MADISON   (United States)

Author keywords

Mfold; Picornavirus; RNA modeling; Secondary structure prediction; Topology

Indexed keywords

VIRUS RNA;

ALGORITHM; ARTICLE; NONHUMAN; PHYLOGENY; PICORNAVIRUS; RNA SEQUENCE; RNA STRUCTURE; STATISTICAL ANALYSIS; VIRUS GENOME;

CARDIOVIRUS; ENTEROVIRUS; PICORNAVIRIDAE; RNA VIRUSES;

EID: 0031427630     PISSN: 10445773     EISSN: None     Source Type: Journal    
DOI: 10.1006/smvy.1997.0126     Document Type: Article

References (13)

1. Zuker M. On finding all suboptimal foldings of an RNA molecule. Science. 244:1989;48-52.
2. M. Zuker, 1994, Prediction of RNA secondary structure by energy minimization, Methods in Molecular Biology, 267, 294, Humana Press, Clifton, NJ.
3. Devereux J., Haeberli P., Smithies O. A comprehensive set of sequence analysis programs for the VAX. Nucleic Acids Res. 12:1984;387-395.
4. Jaeger J. A., Turner D. H., Zuker M. Improved predictions of secondary structure for RNA. Proc. Natl. Acad. Sci. USA. 86:1989;7706-7710.
5. A. B. Jacobson, D. Mills, M. Zuker, 1997, RNA secondary structures throughout a 850 nucleotide domain regulate replicase expression in coliphage Qbeta.
6. Zuker M., Jacobson A. B. Well-determined regions in RNA secondary structure prediction: Analysis of small subunit ribosomal RNA. Nucleic Acids Res. 23:1995;2791-2798.
7. Jacobson A. B., Zuker M. Structural analysis by energy dot plot of a large mRNA. J. Mol. Biol. 233:1993;261-269.
8. Bruccoleri R. E., Heinrich G. An improved algorithm for nucleic secondary structure display. Comput. Appl. Biosci. 4:1988;167-173.
9. Martin L. R., Palmenberg A. C. Tandem Mengo virus 5′ pseudoknots are linked to vRNA synthesis, not poly(C)-mediated virulence. J. Virol. 70:1996;8182-8186.
10. Duke G. M., Hoffman M. A., Palmenberg A. C. Sequence and structural elements that contribute to efficient encephalomyocarditis viral RNA translation. J. Virol. 66:1992;1602-1609.
11. Mirmomeni M. H., Hughes P. J., Stanway G. An RNA tertiary structure in the 3′ untranslated region of enteroviruses is necessary for efficient replication. J. Virol. 71:1997;2363-2370.
12. Le S. Y., Zuker M. Common structures of the 5′ non-coding RNA in enteroviruses and rhinoviruses: Thermodynamical stability and statistical significance. J. Mol. Biol. 216:1990;729-741.
13. Rowe C. L., Fleming J. O., Nathan M. J., Sgro J.-Y., Palmenberg A. C., Baker S. C. Generation of coronavirus spike deletion variants (SVDs) by high frequency recombination of predicted RNA secondary structure. J. Virol. 71:1997;6183-6190.