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similarity plot analysis simplot v3.5.1  (Simplot Science)

 
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    Simplot Science similarity plot analysis simplot v3.5.1
    Similarity Plot Analysis 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/similarity+plot+simplot+v3%2E5%2E1/pmc11778783-94-10-10?v=Simplot+Science
    Average 90 stars, based on 1 article reviews
    similarity plot analysis simplot v3.5.1 - by Bioz Stars, 2026-07
    90/100 stars

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    <t>Recombination</t> analyses on SD2020 genome. ( A ) Recombination analysis was conducted and a similarity map was generated by Simplot 3.5.1 software with window size of 200 bp and step size of 20 bp. SD2020 as query sequence, was used in similarity plot analysis. ( B ) Schematic diagram of SD2020 PRRSV genomes. ( C ) Recombination regions were shown with segments of different colors and the four recombination breakpoints were detected by RDP v4.1016. Red segments represent the sequence of VR-2332 strain. Blue segment represents the sequence of JXA1-P80 strain. Green segment represents the sequence of JXA1 strain. ( D ) Individual phylogenies reconstructed from non-recombinant fragments identified by RDP v4.1016, with the JXA1-like strain labelled with a blue background and the VR2332 strain labelled with a red background. The phylogenetic tree was constructed by using the neighbor-joining method with 1000 bootstrap replicates in the PHYLIP 3.65 software package.
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    Recombination analyses on SD2020 genome. ( A ) Recombination analysis was conducted and a similarity map was generated by Simplot 3.5.1 software with window size of 200 bp and step size of 20 bp. SD2020 as query sequence, was used in similarity plot analysis. ( B ) Schematic diagram of SD2020 PRRSV genomes. ( C ) Recombination regions were shown with segments of different colors and the four recombination breakpoints were detected by RDP v4.1016. Red segments represent the sequence of VR-2332 strain. Blue segment represents the sequence of JXA1-P80 strain. Green segment represents the sequence of JXA1 strain. ( D ) Individual phylogenies reconstructed from non-recombinant fragments identified by RDP v4.1016, with the JXA1-like strain labelled with a blue background and the VR2332 strain labelled with a red background. The phylogenetic tree was constructed by using the neighbor-joining method with 1000 bootstrap replicates in the PHYLIP 3.65 software package.

    Journal: Viruses

    Article Title: Recombination and Mutation in a New HP-PRRSV Strain (SD2020) from China

    doi: 10.3390/v15010165

    Figure Lengend Snippet: Recombination analyses on SD2020 genome. ( A ) Recombination analysis was conducted and a similarity map was generated by Simplot 3.5.1 software with window size of 200 bp and step size of 20 bp. SD2020 as query sequence, was used in similarity plot analysis. ( B ) Schematic diagram of SD2020 PRRSV genomes. ( C ) Recombination regions were shown with segments of different colors and the four recombination breakpoints were detected by RDP v4.1016. Red segments represent the sequence of VR-2332 strain. Blue segment represents the sequence of JXA1-P80 strain. Green segment represents the sequence of JXA1 strain. ( D ) Individual phylogenies reconstructed from non-recombinant fragments identified by RDP v4.1016, with the JXA1-like strain labelled with a blue background and the VR2332 strain labelled with a red background. The phylogenetic tree was constructed by using the neighbor-joining method with 1000 bootstrap replicates in the PHYLIP 3.65 software package.

    Article Snippet: The recombination analysis (similarity plot in SIMPLOT v3.5.1) supported that the SD2020 has a recombinant genome ( A).

    Techniques: Generated, Software, Sequencing, Recombinant, Construct