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bootscan analysis  (Simplot Science)

 
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    Simplot Science bootscan analysis
    Bootscan Analysis, supplied by Simplot Science, used in various techniques. Bioz Stars score: 86/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/product/bootscanning+approach+with+simplot+software/analysis+bootscan/pm41012690-4-4-6
    Average 86 stars, based on 1 article reviews
    bootscan analysis - by Bioz Stars, 2026-11
    86/100 stars

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    Related Articles

    Recombinant:

    Article Title: Epidemiological dynamics and molecular characteristics of HIV-1 among transgender women in the Central-West region of Brazil
    Article Snippet: .. Potential recombinant sequences were identified using a bootscan analysis in the SimPlot version 3.5.1 program (sliding window of 200 bp, step size of 10 bp). ..

    Article Title: Epidemiological dynamics and molecular characteristics of HIV-1 among transgender women in the Central-West region of Brazil.
    Article Snippet: .. Potential recombinant sequences were identified using a bootscan analysis in the SimPlot version 3.5.1 program (sliding window of 200 bp, step size of 10 bp). ..

    other:

    Article Title: Phylogenetic Characteristics and High Prevalence of a Merbecovirus in Hedgehogs from Greenspace of a Metropolis, China
    Article Snippet: To assess potential recombination events in the genomes of hedgehog CoVs identified in this study, Bootscan analysis was performed using SimPlot (v3.5.1; SCRoftware, Johns Hopkins University School of Medicine, Baltimore, MD, USA) with a 1000 bp sliding window and 200 bp step size, based on the Kimura two-parameter model and the Neighbor-Joining method.

    Sequencing:

    Article Title: Adaptive Evolution and Distinct Mutation Signatures of Full‐Length HBV Quasispecies in HBeAg‐Negative Chronic Hepatitis B
    Article Snippet: .. Using RDP4 results, the major and minor parental quasispecies sequences, together with one reference genotype C and one genotype H sequence from NCBI, were selected for BootScan analysis using SimPlot to validate intrahost recombination. ..



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    bootscanning approach with simplot software  (Simplot Science)
    90
    Simplot Science bootscanning approach with simplot software
    Recombination between serum and foreskin. (A) A phylogenetic network is shown containing four serum and six foreskin sequences from patient N18674. The Phi test for recombination was significant at p=0.005. Removal of one of the serum sequences resulted in the phylogenetic network shown in (B) and an insignificant Phi test of p=0.1. (C) All sequences in (A) were subjected to <t>bootscanning,</t> with the suspected recombinant used as the query sequence. Colored circles in (A) correspond to the colors representing high bootscanning values in (C). (D) A subset of the V4 domain alignment from a patient with highly segregated serum and foreskin sequences is shown (N17873). A consensus sequences for the entire alignment is followed by two serum and three foreskin sequences. Glycosylation motifs are highlighted in the consensus sequence. A potential case of recombination between serum and foreskin in V4 is highlighted in sequence P-N17873_3_10.
    Bootscanning Approach With Simplot Software, supplied by Simplot Science, used in various techniques. Bioz Stars score: 90/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/product/bootscanning+approach+with+simplot+software/bootscanning+analysis+simplot+3+5+1/pmc03380386-103-21-24
    Average 90 stars, based on 1 article reviews
    bootscanning approach with simplot software - by Bioz Stars, 2026-11
    90/100 stars
    		  Buy from Supplier

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    Recombination between serum and foreskin. (A) A phylogenetic network is shown containing four serum and six foreskin sequences from patient N18674. The Phi test for recombination was significant at p=0.005. Removal of one of the serum sequences resulted in the phylogenetic network shown in (B) and an insignificant Phi test of p=0.1. (C) All sequences in (A) were subjected to bootscanning, with the suspected recombinant used as the query sequence. Colored circles in (A) correspond to the colors representing high bootscanning values in (C). (D) A subset of the V4 domain alignment from a patient with highly segregated serum and foreskin sequences is shown (N17873). A consensus sequences for the entire alignment is followed by two serum and three foreskin sequences. Glycosylation motifs are highlighted in the consensus sequence. A potential case of recombination between serum and foreskin in V4 is highlighted in sequence P-N17873_3_10.

    Journal: AIDS Research and Human Retroviruses

    Article Title: HIV Type 1 Genetic Variation in Foreskin and Blood from Subjects in Rakai, Uganda

    doi: 10.1089/aid.2011.0176

    Figure Lengend Snippet: Recombination between serum and foreskin. (A) A phylogenetic network is shown containing four serum and six foreskin sequences from patient N18674. The Phi test for recombination was significant at p=0.005. Removal of one of the serum sequences resulted in the phylogenetic network shown in (B) and an insignificant Phi test of p=0.1. (C) All sequences in (A) were subjected to bootscanning, with the suspected recombinant used as the query sequence. Colored circles in (A) correspond to the colors representing high bootscanning values in (C). (D) A subset of the V4 domain alignment from a patient with highly segregated serum and foreskin sequences is shown (N17873). A consensus sequences for the entire alignment is followed by two serum and three foreskin sequences. Glycosylation motifs are highlighted in the consensus sequence. A potential case of recombination between serum and foreskin in V4 is highlighted in sequence P-N17873_3_10.

    Article Snippet: If the signal for recombination was significant (Phi test p -value<0.05), the sequence population was checked for recombination breakpoints using a bootscanning approach with SimPlot software ( http://sray.med.som.jhmi.edu/SCRoftware/simplot/ ).

    Techniques: Recombinant, Sequencing, Glycoproteomics