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bootscanning approach in simplot version 3.5.1  (Simplot Science)

 
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    Simplot Science bootscanning approach in simplot version 3.5.1
    Bootscanning Approach In Simplot Version 3.5.1, 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/result/bootscanning approach in simplot version 3.5.1/product/Simplot Science
    Average 90 stars, based on 1 article reviews
    bootscanning approach in simplot version 3.5.1 - by Bioz Stars, 2026-04
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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 <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.
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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 <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.
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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