Nucleotide substitutions in dengue virus serotypes from Asian and American countries: insights into intracodon recombination and purifying selection
Eck Institute for Global Health, Department of Biological Sciences, University of Notre Dame, 46556, Notre Dame, IN, USA
BMC Microbiology 2013, 13:37 doi:10.1186/1471-2180-13-37Published: 14 February 2013
Additional file 1: Table S1:
List of GenBank accession numbers of dengue virus samples investigated in the study. The country and year of collection of samples are also provided.
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Additional file 2: Table S2:
Relative rate of nucleotide substitutions (based on HKY85 model) within serotypes of dengue virus.
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Additional file 3: Table S3:
Distribution of synonymous (syn) and non-synonymous (non-syn) sites among different genes of dengue virus. The numbers in parenthesis are counts of substitutions that are fixed within serotypes. The p value shows statistical significance of association between synonymous or nonsynonymous sites with or without tendency of fixation in each gene.
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Additional file 4:
Codons that are used more often than expected in one sample (RSCU >2 *) but less than expected (RSCU < 0.5) in the other in the same serotype of dengue virus.
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Additional file 5: Figure S1:
Condon context patterns of DENV 1, 2, 3 and 4.
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Additional file 6:
List of positively and negatively selected sites in dengue virus genes.
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