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bootscanning analysis using simplot v3.5.1  (Simplot Science)

 
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    Simplot Science bootscanning analysis using simplot v3.5.1
    Bootscanning Analysis Using Simplot V3.5.1, 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/product/simplot+bootscan+analysis/bootscanning+analysis+simplot+3+5+1/pmc03733632-100-13-12
    Average 90 stars, based on 1 article reviews
    bootscanning analysis using simplot v3.5.1 - by Bioz Stars, 2026-10
    90/100 stars

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    Related Articles

    other:

    Article Title: Multiple CRF01_AE/CRF07_BC Recombinants Enhanced the HIV-1 Epidemic Complexity Among MSM in Shenyang City, Northeast China
    Article Snippet: Recombination fragments (as determined using jpHMM and Simplot bootscanning) were phylogenetically studied using IQ-Tree v2.0.5.

    Article Title: Genetic Dynamic Analysis of the Influenza A H5N1 NS1 Gene in China
    Article Snippet: For each sample, the eight gene segment alignments were manually concatenated in the order of their length to generate a single alignment of full genome sequences, and the resulting alignment was analyzed using the bootscanning method implemented in the SimPlot v3.5.1 .

    Article Title: Identification of a novel CRF01_AE/CRF07_BC (CRF163_0107) circulating recombinant form in Shenyang city, the economic center of Northeast China.
    Article Snippet: Bootscanning in Simplot (version 3.5.1) and RIP online tools(RIP 3.0 submission form (lanl.gov)) analyses were used to identify the recombination patterns.

    Article Title: Phylodynamics of HIV-1 Circulating Recombinant Forms 12_BF and 38_BF in Argentina and Uruguay
    Article Snippet: Two strategies were used to characterize the HIV-1 pol sequences used in the present study as CRF12_BF-like or CRF38_BF-like recombinants: 1) First, the recombination breakpoints of each sequence were identified by Bootscanning using Simplot version 3.5.1 [ ].

    Article Title: Phylodynamics of HIV-1 Subtype C Epidemic in East Africa
    Article Snippet: Putative intrasubtype C/C′ recombinant sequences in Ethiopia were identified by Bootscanning using Simplot version 3.5.1 , following the same procedure described by Pollakis et al . Bootstrap values supporting branching with reference sequences were determined in Neighbor-Joining (NJ) trees constructed using the K2-P nucleotide substitution model, based on 100 re-samplings, with a 300 bp sliding window moving in steps of 10 bases.

    Software:

    Article Title: HIV-1 genetic diversity and transmitted drug resistance among newly diagnosed HIV-1 individuals in Jiangmen, China.
    Article Snippet: Correspondence Guifang Hu, School of Public Health, Southern Medical University, No.1023, South Shatai Road, Baiyun District, Guangzhou, Guangdong 510515, China Telephone number: +86-18933940199 E-mail: guif_hu@sina.com Funding information Guangdong Province Public Welfare Research and Capacity Building Project, Grant number: 2014B020212007; Guangzhou Science and Technology Project, Grant number: 201508020018



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    Similarity plot analysis comparing strain Ningxia echovirus 30 (E30) with enterovirus B (EV-B) strains, based on the full-length genomes. The 2017 E30 strains were used independently as query sequences. The nucleotide sequence of each strain was compared with those of strains of EV-B, using Simplot software version 3.5.1, with a sliding window of 200 nucleotides moving in steps of 20. Colored lines indicate the strains described in this article, and other strains are indicated by gray lines. The whole genome Simplot BootScan analysis was conducted with the query sequence of NX2017E30 strain. A) The enterovirus genomic organization is shown at the top. B) Similarity plot analysis. C) Bootscanning analysis on the putative recombinant strain and its parental sequences.

    Journal: Biosafety and Health

    Article Title: Genetic characterizations and molecular epidemiology of human echovirus 30 isolated from Ningxia, China

    doi: 10.1016/j.bsheal.2023.10.001

    Figure Lengend Snippet: Similarity plot analysis comparing strain Ningxia echovirus 30 (E30) with enterovirus B (EV-B) strains, based on the full-length genomes. The 2017 E30 strains were used independently as query sequences. The nucleotide sequence of each strain was compared with those of strains of EV-B, using Simplot software version 3.5.1, with a sliding window of 200 nucleotides moving in steps of 20. Colored lines indicate the strains described in this article, and other strains are indicated by gray lines. The whole genome Simplot BootScan analysis was conducted with the query sequence of NX2017E30 strain. A) The enterovirus genomic organization is shown at the top. B) Similarity plot analysis. C) Bootscanning analysis on the putative recombinant strain and its parental sequences.

    Article Snippet: The whole genome Simplot BootScan analysis was conducted with the query sequence of NX2017E30 strain.

    Techniques: Sequencing, Software, Recombinant