Skip to main content
Article thumbnail
Location of Repository

Extensive purifying selection acting on synonymous sites in HIV-1 Group M sequences

By Nobubelo K Ngandu, Konrad Scheffler, Penny Moore, Zenda Woodman, Darren Martin and Cathal Seoighe
Topics: Research
Publisher: BioMed Central
OAI identifier: oai:pubmedcentral.nih.gov:2666660
Provided by: PubMed Central
Download PDF:
Sorry, we are unable to provide the full text but you may find it at the following location(s):
  • http://www.pubmedcentral.nih.g... (external link)
  • Suggested articles

    Citations

    1. (2000). A compilation of cellular transcription factor interactions with the HIV-1 LTR promoter. Nucleic Acids Res
    2. A human immunodeficiency virus type 1-infected individual with low viral load harbors a virus variant that exhibits an in vitro RNA dimerization defect. JV i r o l2004,
    3. A large variation in the rates of synonymous substitution for RNA viruses and its relationship to a diversity of viral infection and transmission modes. M o lB i o lE v o l2004,
    4. (2001). A second exon splicing silencer within human immunodeficiency virus type 1 tat exon 2 represses splicing of Tat mRNA and binds protein hnRNP H.
    5. (2006). A suboptimal 5' splice site downstream of HIV-1 splice site A1 is required for unspliced viral mRNA accumulation and efficient virus replication. Retrovirology
    6. Am o d e l of directional selection applied to the evolution of drug resistance in HIV-1. M o lB i o lE v o l2007,
    7. (2006). Automated Phylogenetic Detection of Recombination Using a Genetic Algorithm. Mol Biol Evol
    8. (2004). Binding, bending and bonding': polypurine tract-primed initiation of plus-strand DNA synthesis in human immunodeficiency virus.
    9. Burny A and Verdin E: A transcriptional regulatory element is associated with a nuclease-hypersensitive site in the pol gene of human immunodeficiency virus type 1. JV i r o l1994,
    10. Cloning and functional analysis of multiply spliced mRNA species of human immunodeficiency virus type 1. JV i r o l1990,
    11. (2000). Codonsubstitution models for heterogeneous selection pressure at amino acid sites. Genetics
    12. Comparative study of adaptive molecular evolution in different human immunodeficiency virus groups and subtypes. JV i r o l2004,
    13. (2004). Coovadia HM and Cassol S: Mapping sites of positive selection and amino acid diversification in the HIV genome: an alternative approach to vaccine design?. Genetics
    14. (2007). CTL response to HIV type 1 subtype C is poorly predicted by known epitope motifs. AIDS Res Hum Retroviruses
    15. (2000). Detecting hypermutations in viral sequences with an emphasis on G –> A hypermutation. Bioinformatics
    16. (2005). Effect of polypurine tract (PPT) mutations on human immunodeficiency virus type 1 replication: a virus with a completely randomized PPT retains low infectivity. JV i r o l
    17. (2003). Effect of recombination on the accuracy of the likelihood method for detecting positive selection at amino acid sites. Genetics
    18. Env and Vpu proteins of human immunodeficiency virus type 1 are produced from multiple bicistronic mRNAs. JV i r o l1990,
    19. (2001). Evidence for purifying selection acting on silent sites
    20. (2008). Felber BK and Pavlakis GN: Mutational inactivation of an inhibitory sequence Virology Journal
    21. (1999). Genealogical evidence for positive selection in the nef gene of HIV-1. Genetics
    22. (2008). High-throughput SHAPE analysis reveals structures in HIV-1 genomic RNA strongly conserved across distinct biological states. PLoS Biol
    23. (2005). HyPhy: hypothesis testing using phylogenies. Bioinformatics
    24. (1990). Identification and characterization of an enhancer in the coding region of the genome of human immunodeficiency virus type 1. Proc Natl Acad Sci
    25. Identification and characterization of intragenic sequences which repress human immunodeficiency virus structural gene expression. JV i r o l1991,
    26. In vitro evidence for a long range pseudoknot in the 5'-untranslated and matrix coding regions of
    27. Inactivation of the human immunodeficiency virus type 1 inhibitory elements allows Rev-independent expression of Gag and Gag/protease and particle formation. JV i r o l1997,
    28. Intergrated functional and bioinformatics approach for the identification and experimental verification of RNA signals:
    29. (2003). Kel-Margoulis OV and Wingender E: MATCH: A tool for searching transcription factor binding sites in DNA sequences. Nucleic Acids Res
    30. (1998). Likelihood models for detecting positively selected amino acid sites and applications to the HIV-1 envelope gene. Genetics
    31. (1998). LTR and tat variability of HIV1 isolates from patients with divergent rates of disease progression. Virus Res
    32. Negative and positive mRNA splicing elements act competitively to regulate human immunodeficiency virus type 1 vif gene expression. JV i r o l2008,
    33. Overlapping cis sites used for splicing of HIV-1 env/nef and rev mRNAs.
    34. (2003). Phuphuakrat A and Auewarakul P: Heterogeneity of HIV-1 Rev response element. AIDS Res Hum Retroviruses
    35. (2003). Potential impact of recombination on sitewise approaches for detecting positive natural selection. Genet Res
    36. (1995). Probing the details of the HIV-1 Rev-Revresponsive element interaction: effects of modified nucleotides on protein affinity and conformational changes during complex formation.
    37. RNA secondary structure and binding sites for gag gene products in the 5' packaging signal of human immunodeficiency virus type 1. JV i r o l1995,
    38. (2006). Robust inference of positive selection from recombining coding sequences. Bioinformatics
    39. (2001). Scheid A and Schaal H: Influence of the small leader exons 2 and 3 on human immunodeficiency virus type 1 gene expression. Virology
    40. Sequence and structural determinants required for priming of plus-strand DNA synthesis by the human immunodeficiency virus type 1 polypurine tract. JV i r o l1996,
    41. (2007). SF: Purine analog substitution of the HIV-1 polypurine tract primer defines regions controlling initiation of plus-strand DNA synthesis. Nucleic Acids Res
    42. (2005). Site-to-site variation of synonymous substitution rates. Mol Biol Evol
    43. Specific and independent recognition of U3 and U5 att sites by human immunodeficiency virus type 1 integrase in vivo. JV i r o l1998,
    44. Specificities involved in the initiation of retroviral plus-strand DNA. JV i r o l1990,
    45. Structural change in Rev responsive element RNA of
    46. Structure-based mutagenesis of the human immunodeficiency virus type 1 DNA attachment site: effects on integration and cDNA synthesis. JV i r o l1999,
    47. (2007). Taveira N and Rambaut A: Synonymous substitution rates predict HIV disease progression as a result of underlying replication dynamics. PLoS Comput Biol
    48. The 5' and 3' TAR elements of human immunodeficiency virus exert effects at several points in the virus life cycle. JV i r o l1998,
    49. (2008). The c3-v4 region is a major target of autologous neutralizing antibodies in human immunodeficiency virus type 1 subtype C infection. JV i r o l
    50. (2000). The crystal structure of the Rev binding element of HIV-1 reveals novel base pairing and conformational variability. Proc Natl Acad Sci USA
    51. The sequence features important for plus strand priming by human immunodeficiency virus type 1 reverse transcriptase.
    52. (2006). The strength of the HIV-1 3' splice sites affects Rev function. Retrovirology
    53. Thiele S and Wingender E: TRANSFAC: transcriptional regulation, from patterns to profiles.
    54. (2005). Transcription factor binding sites in the pol gene intragenic regulatory region of HIV-1 are important for virus infectivity. Nucleic Acids Res
    55. Tse A and Pavlakis GN: The rev (trs/art) protein of human immunodeficiency virus type 1 affects viral mRNA and protein expression via a cis-acting sequence in the env region. JV i r o l1989,

    To submit an update or takedown request for this paper, please submit an Update/Correction/Removal Request.