boot scanning in simplot v3.5.1  (Simplot Science)

Journal: AIDS Research and Human Retroviruses

Article Title: Near-Full-Length Genetic Characterization of a Novel HIV-1 Unique Recombinant with Similarities to A1, CRF01_AE, and CRFO2_AG Viruses in Yaoundé, Cameroon

doi: 10.1089/aid.2019.0042

Figure Lengend Snippet: Recombination events and breakpoints identified in NACMR092. (A) Recombinant breakpoint positions were calculated by boot scanning analysis using Simplot v3.5.1, as described. The percentages of permuted trees (y-axis) of the subtypes at each sequence position (x-axis) are shown. (B) Genomic map of the near-full-length sequence of NACMR092 (based on HXB2 numbering). The mosaic map was generated using the Los Alamos Recombinant HIV-1 Drawing Tool (https://hiv.lanl.gov/content/sequence/DRAW_CRF/recom_mapper.html). The start (nucleotide 874) and end (nucleotide 9403) of the near-full-length sequence, as well as the breakpoints are shown. Genomic sequences originating from HIV-1 subtype A1 (grey color), CRF01_AE (red color), and CRF02_AG (blue color) are shown. LTR, long-terminal repeat; gag, group-specific antigen; pol, polymerase; vif, viral infectivity factor; vpr, viral protein R; vpu, viral protein U; env, envelope; tat, trans-activator of transcription; nef, negative factor. Color images are available online.

Article Snippet: Fragments I, II, III, IV, V, VI, VII, VIII, and IX of the mosaic genome correspond, respectively, to nucleotides 874–1526, 1527–1826, 1827–5029, 5030–5629, 5630–6629, 6630–6862, 6863–8862, 8863–9106, and nucleotides 9107–9403 of the HXB2 genome. fig ft0 fig mode=article f1 fig/graphic|fig/alternatives/graphic mode="anchored" m1 Open in a separate window FIG. 2. caption a7 Recombination events and breakpoints identified in NACMR092. (A) Recombinant breakpoint positions were calculated by boot scanning analysis using Simplot v3.5.1, as described.

Techniques: Recombinant, Sequencing, Generated, Genomic Sequencing, Infection

Journal: BMC Research Notes

Article Title: Surveillance of transmitted HIV-1 antiretroviral drug resistance in the context of decentralized HIV care in Senegal and the Ebola outbreak in Guinea

doi: 10.1186/s13104-018-3804-9

Figure Lengend Snippet: Phylogenetic inference of HIV-1 protease and partial reverse transcriptase sequences from antiretroviral-naïve patients in Senegal. Maximum likelihood analysis, implemented with the PhyML standalone package v3.1, involved 89 nucleotide sequences covering 1026 positions in the final dataset. Branch lengths are measured in the number of substitutions per site. The percentage of trees (SH-aLRT) in which the associated taxa clustered together is shown and values ≥ 85 were significant. The “Cx” clade indicates a possible transmission network between two men (self-reported homosexual and heterosexual). Some clades were collapsed for clarity. Diamond triangles are study field isolates (right panel), of which those with three stars*** are unique recombinant forms (URFs). The left panel depicts boot-scanning plots for each URF queried against representative HIV-1 reference sequences obtained from the Los Alamos HIV database ( https://www.hiv.lanl.gov ). These sequences are color coded and included A3, CRF02_AG, F1, F2, B, D, CRF06_CPX, A1, K, C, H. Genomic splits or breakpoints were confirmed by reconstruction of phylogenetic trees focused on those unbroken regions (not shown). Boot-scanning was generated in SimPlot v3.5.1 under the Neighbor-Joining algorithm, modelled with the Kimura two-parameter and 100 bootstrap replicates (percentage of permuted trees on the y-axis). Boot-scanning was run with parameters of 50% consensus sequences, 300 base-pair window size, 10 base-pair step size (nucleotides position on the x-axis), and a nucleotide transition/transversion ratio of 2.0

Article Snippet: Patterns of recombination, notably for outliers, divergent and, long-branch sequences, were determined through Boot-scanning using SimPlot v3.5.1.

Techniques: Transmission Assay, Recombinant, Generated