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bootscan analysis simplot program version 3.5.1  (Simplot Science)

 
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    Structured Review

    Simplot Science bootscan analysis simplot program version 3.5.1
    <t>Bootscan</t> analysis of recombinant CAstV sequences for confirming recombination was performed using Simplot program v3.5.1. Each analysis considers different parent sequences (different colors) plotted in a graph considering in the vertical-axis Percentage of permuted trees, and on the horizontal axis, position on the genome of the query sequence. Recombinant CAstV query sequences are 19-0981/CA-SK/19 ; Biii-ANAND/IN/2016 ; Bi-GDYHTJ718-6/CN/2018 ; 18-0942/CA-SK/18 ; 19-0935/CA-SK/19 ; CC_CkAstV/US/2014 ; and Bii-GA2011/US/2011 .
    Bootscan Analysis Simplot Program 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/product/bootscan+analysis+simplot+program+version+3%2E5%2E1/bootscan+analysis+simplot+version+3+5+1/pmc07600043-178-8-12
    Average 90 stars, based on 1 article reviews
    bootscan analysis simplot program version 3.5.1 - by Bioz Stars, 2026-11
    90/100 stars

    Images

    1) Product Images from "Chicken Astrovirus (CAstV) Molecular Studies Reveal Evidence of Multiple Past Recombination Events in Sequences Originated from Clinical Samples of White Chick Syndrome (WCS) in Western Canada"

    Article Title: Chicken Astrovirus (CAstV) Molecular Studies Reveal Evidence of Multiple Past Recombination Events in Sequences Originated from Clinical Samples of White Chick Syndrome (WCS) in Western Canada

    Journal: Viruses

    doi: 10.3390/v12101096

    Bootscan analysis of recombinant CAstV sequences for confirming recombination was performed using Simplot program v3.5.1. Each analysis considers different parent sequences (different colors) plotted in a graph considering in the vertical-axis Percentage of permuted trees, and on the horizontal axis, position on the genome of the query sequence. Recombinant CAstV query sequences are 19-0981/CA-SK/19 ; Biii-ANAND/IN/2016 ; Bi-GDYHTJ718-6/CN/2018 ; 18-0942/CA-SK/18 ; 19-0935/CA-SK/19 ; CC_CkAstV/US/2014 ; and Bii-GA2011/US/2011 .
    Figure Legend Snippet: Bootscan analysis of recombinant CAstV sequences for confirming recombination was performed using Simplot program v3.5.1. Each analysis considers different parent sequences (different colors) plotted in a graph considering in the vertical-axis Percentage of permuted trees, and on the horizontal axis, position on the genome of the query sequence. Recombinant CAstV query sequences are 19-0981/CA-SK/19 ; Biii-ANAND/IN/2016 ; Bi-GDYHTJ718-6/CN/2018 ; 18-0942/CA-SK/18 ; 19-0935/CA-SK/19 ; CC_CkAstV/US/2014 ; and Bii-GA2011/US/2011 .

    Techniques Used: Recombinant, Sequencing

    CAstV recombinant sequences and parents/parent-like sequences detected by 6 recombination methods in RDP5, ML phylogenetic trees, and Bootscan analysis in SimPlot software.
    Figure Legend Snippet: CAstV recombinant sequences and parents/parent-like sequences detected by 6 recombination methods in RDP5, ML phylogenetic trees, and Bootscan analysis in SimPlot software.

    Techniques Used: Recombinant, Software, Sequencing

    Related Articles

    Isolation:

    Article Title: Uncovering the Prevalence and Genetic Characterization of Rabbit-Derived Paslahepevirus Balayani (Hepatitis E Virus) in Hebei Province, China.
    Article Snippet: Paslahepevirus balayani (hepatitis E virus) is a zoonotic pathogen, with rabbit Paslahepevirus balayani (HEV-3ra) being widely distributed among global rabbit populations.. Notably, in China, rabbits constitute a significant HEV host, second only to swine.. Emerging evidence suggests that HEV-3ra possesses the capability to cross species barriers and infect humans.

    Immunofluorescence:

    Article Title: Discovery of a novel Betacoronavirus 1, cpCoV, in goats in China: The new risk of cross-species transmission.
    Article Snippet: .. Bootscan analysis was performed with Simplot, version 3.5.1. https://doi.org/10.1371/journal.ppat.1012974.g003 PLOS Pathogens | https://doi.org/10.1371/journal.ppat.1012974 March 18, 2025 14 / 23 three blind passages, the challenge group samples induced a CPE, and the cell cultures were identified as cpCoV-positive by RT-qPCR, RT-PCR, and IFA methods. ..

    Software:

    Article Title: Identification of a novel HIV-1 third-generation circulating recombinant form (CRF126_0755) in Guangdong, China.
    Article Snippet: .. Branches with bootstrap values greater than 70% were considered reliable, and the values are shown at the nodes. (B) BootScan analysis, performed using SimPlot 3.5 software with a window size of 300 bp and step size of 20 bp. (C) Genome mosaic map of CRF126_0755 NFLG, generated using the LANL Recombinant HIV-1 Drawing Tool (https:// www. hiv. lanl. gov/ conte nt/ seque nce/ DRAW_ CRF/ recom_ mapper. html) in almost all CRF55_01B strains, was found in all four CRF126-0755 NFLGs, possibly conferring increased drug resistance [17]. ..

    Generated:

    Article Title: Identification of a novel HIV-1 third-generation circulating recombinant form (CRF126_0755) in Guangdong, China.
    Article Snippet: .. Branches with bootstrap values greater than 70% were considered reliable, and the values are shown at the nodes. (B) BootScan analysis, performed using SimPlot 3.5 software with a window size of 300 bp and step size of 20 bp. (C) Genome mosaic map of CRF126_0755 NFLG, generated using the LANL Recombinant HIV-1 Drawing Tool (https:// www. hiv. lanl. gov/ conte nt/ seque nce/ DRAW_ CRF/ recom_ mapper. html) in almost all CRF55_01B strains, was found in all four CRF126-0755 NFLGs, possibly conferring increased drug resistance [17]. ..

    Article Title: Mixed Infections Unravel Novel HCV Inter-Genotypic Recombinant Forms within the Conserved IRES Region.
    Article Snippet: .. Moreover, the Bootscan graphs generated by Simplot software (version 3.5.1) indicated similar results (Figure 3, right panels). ..

    Recombinant:

    Article Title: Identification of a novel HIV-1 third-generation circulating recombinant form (CRF126_0755) in Guangdong, China.
    Article Snippet: .. Branches with bootstrap values greater than 70% were considered reliable, and the values are shown at the nodes. (B) BootScan analysis, performed using SimPlot 3.5 software with a window size of 300 bp and step size of 20 bp. (C) Genome mosaic map of CRF126_0755 NFLG, generated using the LANL Recombinant HIV-1 Drawing Tool (https:// www. hiv. lanl. gov/ conte nt/ seque nce/ DRAW_ CRF/ recom_ mapper. html) in almost all CRF55_01B strains, was found in all four CRF126-0755 NFLGs, possibly conferring increased drug resistance [17]. ..

    other:

    Article Title: Whole-Genome Analysis of Porcine Epidemic Diarrhea Virus from Yunnan, China.
    Article Snippet: The above methods were further validated and confirmed for the presence of genome recombination and break sites using BootScan in Simplot software, with the BootScan window size set to 400 bp, the gap size set to 40 bp, and other parameters set to default values.

    Article Title: Genetic characterization of a novel HIV-1 circulating recombinant form (CRF162_cpx) involving CRF01_AE, CRF07_BC and subtype B in Guangdong, China.
    Article Snippet: Human immunodeficiency virus type 1 (HIV-1) is characterized by its extremely high level of genetic diversity.. The spread of different subtypes in the same population often leads to the emergence of circulating recombinant forms (CRFs) and unique recombinant forms (URFs).. At present, the main recombinant subtypes of HIV-1 in China originate from CRF07_BC, CRF01_AE, CRF55_01B and subtype B.

    Article Title: Identification of a novel HIV-1 third-generation circulating recombinant form (CRF126_0755) in Guangdong, China.
    Article Snippet: The sequences were analyzed using jpHMM (http:// jpHMM. gobics. de/ submi ssion_ hiv. html), RIP (https:// www. hiv. lanl. gov/ conte nt/ seque nce/ RIP/ RIP. html), and BootScan (Simplot software V3.5.1) with a window size of 350 bp and steps of 20 bp.



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    bootscan analysis simplot program version 3.5.1  (Simplot Science)
    90
    Simplot Science bootscan analysis simplot program version 3.5.1
    <t>Bootscan</t> analysis of recombinant CAstV sequences for confirming recombination was performed using Simplot program v3.5.1. Each analysis considers different parent sequences (different colors) plotted in a graph considering in the vertical-axis Percentage of permuted trees, and on the horizontal axis, position on the genome of the query sequence. Recombinant CAstV query sequences are 19-0981/CA-SK/19 ; Biii-ANAND/IN/2016 ; Bi-GDYHTJ718-6/CN/2018 ; 18-0942/CA-SK/18 ; 19-0935/CA-SK/19 ; CC_CkAstV/US/2014 ; and Bii-GA2011/US/2011 .
    Bootscan Analysis Simplot Program 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/product/bootscan+analysis+simplot+program+version+3%2E5%2E1/bootscan+analysis+simplot+version+3+5+1/pmc07600043-178-8-12
    Average 90 stars, based on 1 article reviews
    bootscan analysis simplot program version 3.5.1 - by Bioz Stars, 2026-11
    90/100 stars
    		  Buy from Supplier

    Image Search Results


    Bootscan analysis of recombinant CAstV sequences for confirming recombination was performed using Simplot program v3.5.1. Each analysis considers different parent sequences (different colors) plotted in a graph considering in the vertical-axis Percentage of permuted trees, and on the horizontal axis, position on the genome of the query sequence. Recombinant CAstV query sequences are 19-0981/CA-SK/19 ; Biii-ANAND/IN/2016 ; Bi-GDYHTJ718-6/CN/2018 ; 18-0942/CA-SK/18 ; 19-0935/CA-SK/19 ; CC_CkAstV/US/2014 ; and Bii-GA2011/US/2011 .

    Journal: Viruses

    Article Title: Chicken Astrovirus (CAstV) Molecular Studies Reveal Evidence of Multiple Past Recombination Events in Sequences Originated from Clinical Samples of White Chick Syndrome (WCS) in Western Canada

    doi: 10.3390/v12101096

    Figure Lengend Snippet: Bootscan analysis of recombinant CAstV sequences for confirming recombination was performed using Simplot program v3.5.1. Each analysis considers different parent sequences (different colors) plotted in a graph considering in the vertical-axis Percentage of permuted trees, and on the horizontal axis, position on the genome of the query sequence. Recombinant CAstV query sequences are 19-0981/CA-SK/19 ; Biii-ANAND/IN/2016 ; Bi-GDYHTJ718-6/CN/2018 ; 18-0942/CA-SK/18 ; 19-0935/CA-SK/19 ; CC_CkAstV/US/2014 ; and Bii-GA2011/US/2011 .

    Article Snippet: Putative recombination sequences were further investigated by using Bootscan analysis within the Simplot program version 3.5.1 [ ], using the following parameters: window size = 400 bp; step size = 40 bp; GapStrip = On; Repetitions = 100; Kimura 2-parameter substitution model; T/t = 2; and using the neighbor-joining method [ , , ].

    Techniques: Recombinant, Sequencing

    CAstV recombinant sequences and parents/parent-like sequences detected by 6 recombination methods in RDP5, ML phylogenetic trees, and Bootscan analysis in SimPlot software.

    Journal: Viruses

    Article Title: Chicken Astrovirus (CAstV) Molecular Studies Reveal Evidence of Multiple Past Recombination Events in Sequences Originated from Clinical Samples of White Chick Syndrome (WCS) in Western Canada

    doi: 10.3390/v12101096

    Figure Lengend Snippet: CAstV recombinant sequences and parents/parent-like sequences detected by 6 recombination methods in RDP5, ML phylogenetic trees, and Bootscan analysis in SimPlot software.

    Article Snippet: Putative recombination sequences were further investigated by using Bootscan analysis within the Simplot program version 3.5.1 [ ], using the following parameters: window size = 400 bp; step size = 40 bp; GapStrip = On; Repetitions = 100; Kimura 2-parameter substitution model; T/t = 2; and using the neighbor-joining method [ , , ].

    Techniques: Recombinant, Software, Sequencing