Journal: Viruses

Article Title: Clinical, Laboratory, and Molecular Epidemiology of an Outbreak of Aseptic Meningitis Due to a Triple-Recombinant Echovirus in Ashburton, New Zealand

doi: 10.3390/v14040658

Figure Lengend Snippet: Whole genome Simplot BootScan analysis with the query sequence of strain NZ/Ashburton/17WQ2027G/2017-08-20 (accession number MW586892) compared to Echovirus E6 (accession number KP289439), E11 (accession number KP294524), and E30 (accession number KY888274) reference sequences. ( A ) Similarity plot analysis, ( B ) Bootscanning analysis on the putative recombinant strain and its parental sequences. The enterovirus genomic organization is shown in the top.

Article Snippet: A Simplot BootScan v. 3.5.1 [ ] analysis was applied to a ClustalW alignment of the de novo assembled enterovirus genome MW586892 (strain NZ/Ashburton/17WQ2027G/2017-08-20) with echovirus E6 (isolate E6/P735/2013/China, accession number KP289439), echovirus E11 (strain 520k-YN-CHN-2010, accession number KP294524) and echovirus E30 (strain 14-397 collected 2013, accession number KY888274) sequences.

Techniques: Sequencing, Recombinant

Journal: PLoS ONE

Article Title: Analysis of HIV-1 Protease Gene Reveals Frequent Multiple Infections Followed by Recombination among Drug Treated Individuals Living in São Paulo and Santos, Brazil

doi: 10.1371/journal.pone.0084066

Figure Lengend Snippet: We used the Neighbor-Joining method with K2P and 1000 bootstrap replicates. This analysis was performed using the software Simplot v3.5.1, with a window of 75 bp and 5 bp increments.

Article Snippet: Inter-subtype recombinants and breakpoints were investigated using Bootscan as implemented in the Simplot package v3.5.1 .

Techniques: Software

Journal: Viruses

Article Title: Ten Previously Unassigned Human Cosavirus Genotypes Detected in Feces of Children with Non-Polio Acute Flaccid Paralysis in Nigeria in 2020

doi: 10.3390/v17060844

Figure Lengend Snippet: Bootscan analysis showing recombination events in the HCoSV-E sequences. Analysis was conducted using the suspected recombinant sequences as queries ( A – F ) against reference HCoSV species HCoSV-A, HCoSV-B, HCoSV-D, HCoSV-E and HCoSV-F. A single breakpoint between P1 and P2 genomic regions was observed.

Article Snippet: Simplot and Bootscan analyses were conducted using sequences from Database 1 in SimPlot v3.5.1 [ ].

Techniques: Recombinant

Journal: Frontiers in Microbiology

Article Title: Identification and characterization of multiple novel picornaviruses in fecal samples of bar-headed goose

doi: 10.3389/fmicb.2024.1440801

Figure Lengend Snippet: Recombination and phylogenetic analysis of megriviruses from bar-headed geese. (A) BOOTSCAN evidence for the recombination origin on the basis of pairwise distance, modeled with a window size 200, step size 20, and 100 Bootstrap replicates. (B) Neighbor-joining tree constructed using the region of 1–5,133 nt and 8,105–10,644 nt. (C) Neighbor-joining tree constructed using the region of 5,134–8,104 nt. Neighbor-joining method based on 1,000 replicates using MEGA-X software.

Article Snippet: Further recombinant analysis is performed using the BootScan program in the SimPlot software v3.5.1.

Techniques: Construct, Software

Journal: PLoS ONE

Article Title: Analysis of HIV-1 Protease Gene Reveals Frequent Multiple Infections Followed by Recombination among Drug Treated Individuals Living in São Paulo and Santos, Brazil

doi: 10.1371/journal.pone.0084066

Figure Lengend Snippet: The number of times that a particular subtype or recombinant was found in a patient is shown inside the parenthesis to the left of each structure. Break points were mapped according to Bootscan and their positions in base pairs are followed by the number they appeared on mosaic structures (inside the parenthesis).

Article Snippet: Inter-subtype recombinants and breakpoints were investigated using Bootscan as implemented in the Simplot package v3.5.1 .

Techniques: Recombinant