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  • Articles: DFG German National Licenses  (3)
  • 1995-1999  (3)
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  • Articles: DFG German National Licenses  (3)
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Year
Keywords
  • 1
    Electronic Resource
    Electronic Resource
    A method for determining the position and size of optimal sequence regions for phylogenetic analysis (1995)
    Springer
    Journal of molecular evolution 41 (1995), S. 1128-1138 
    Details
    ISSN: 1432-1432
    Keywords: Phylogeny ; Neighbor joining method ; Bootstrap ; Optimal size ; Optimal position ; Nonrandom sequence ; Information ; Foot-and-mouth disease virus
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract The availability of fast and accurate sequencing procedures along with the use of PCR has led to a proliferation of studies of variability at the molecular level in populations. Nevertheless, it is often impractical to examine long genomic stretches and a large number of individuals at the same time. In order to optimize this kind of study, we suggest a heuristic procedure for detection of the shortest region whose informational content can be considered sufficient for significant phylogenetic reconstruction. The method is based on the comparison of the pairwise genetic distances obtained from a set of sequences of reference to those obtained for different windows of variable size and position by means of a simple index. We also present an approach for testing whether the informative content in the stretches selected in this way is significantly different from the corresponding content shown by the larger genomic regions used as reference. Application of this test to the analysis of the VP1 protein gene of foot-and-mouth-disease type C virus allowed us to define optimal stretches whose informative content is not significantly different from that displayed by the complete VP1 sequence. We showed that the predictions made for type C sequences are valid for type O sequences, indicating that the results of the procedure are consistent.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1007/BF00173194
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    Paper (German National Licenses)
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  • 2
    Electronic Resource
    Electronic Resource
    A strain-type clustering of potato virus Y based on the genetic distance between isolates calculated by RFLP analysis of the amplified coat protein gene (1996)
    Springer
    Archives of virology 141 (1996), S. 2425-2442 
    Details
    ISSN: 1432-8798
    Source: Springer Online Journal Archives 1860-2000
    Topics: Medicine
    Notes: Summary Potato virus Y (PVY) isolates have been classified into genetic strains by a host-independent criterion using a molecular typing method. The method used extracts from infected tissue, and included immunocapture-RT-PCR-RFLP analysis using 5 different restriction endonucleases (Dde I,Eco RV,Hinf I,Rsa I andTaq I). Genetic distances between the different PVY “restrictotypes” were calculated and used to define the PVY genetic strains. Three main clusters were found: PVYO, PVYN, and non-potato PVY (PVYNP), in good agreement with classical PVY strain definitions that combine different biological criteria. Our approach was incomparably quicker and more reliable and reproducible than biotyping. The potential of this approach for very quick, simple and automatable molecular epidemiological studies is discussed.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1007/BF01718641
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    Paper (German National Licenses)
    Fulltext
  • 3
    Electronic Resource
    Electronic Resource
    Sequence analysis of HIV-1vif gene in Spanish isolates (1995)
    Springer
    Virus genes 9 (1995), S. 283-288 
    Details
    ISSN: 1572-994X
    Keywords: HIV-1 ; Vif ; nucleotide sequence ; variability
    Source: Springer Online Journal Archives 1860-2000
    Topics: Medicine
    Notes: Abstract We have determined the nucleotide sequence of the HIV-1vif gene in viruses obtained from symptomatic patients of distinct risk groups in Madrid. The genetic diversity among the isolates was estimated in 4.6% (±1.4 standard deviation), a similar value to that obtained for thegag gene 3.9% (±0.8 standard deviation) andenv 4.1% (±1 standard deviation) (Rojas et al., Virus Res31, 331–342, 1994). Amino acid sequence analysis revealed the presence of hypermutable residues at positions 101 and 167, close to antigenically relevant sequential epitopes (comprising amino acids 87–94 and 172–178). Phylogenetic analysis supports the existence of two virus lineages circulating preferentially within different risk groups.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1007/BF01702884
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    Paper (German National Licenses)
    Fulltext
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