bootscan tool simplot version 3.5.1  (Simplot Science)

Journal: mBio

Article Title: Gene duplication, gene loss, and recombination events with variola virus shaped the complex evolutionary path of historical American horsepox-based smallpox vaccines

doi: 10.1128/mbio.01887-23

Figure Lengend Snippet: Similarity profile of the central conserved region of the genomes of historical smallpox vaccines. ( A ) The multialignment of an expanded central conserved region (spanning from the F7L to A36R orthologs) of the six historical smallpox vaccines and HPXV_MNR-76 was scanned for percent similarity using Simplot, using the HPXV_MNR-76 sequence as query, window size 1,200, step size 120. Black arrows indicate the regions of least similarity between VK02 and all other genomes. The asterisk indicates a region of least similarity of all vaccines relative to HPXV_MNR-76. ( B ) The multialignment included five variola virus strains and removed all historical vaccines, except VK02 and VK08. Similar parameters were chosen, but VK02 was selected as the query. The black arrows indicate the regions of least similarity between VK02 and HPXV and VK08, and of high similarity between VK02 and variola virus. Numbers refer to the regions chosen for the Bootscan analysis, from 20 kb to 85 kb of the alignment.

Article Snippet: Putative recombination regions were analyzed using the Bootscan tool implemented in Simplot v.3.5.1 with the same parameters described above and the neighbor-joining tree model.

Techniques: Vaccines, Sequencing, Virus

Journal: mBio

Article Title: Gene duplication, gene loss, and recombination events with variola virus shaped the complex evolutionary path of historical American horsepox-based smallpox vaccines

doi: 10.1128/mbio.01887-23

Figure Lengend Snippet: Recombinant regions in the central conserved region of the VK02 genome. The region between 20 kb and 85 kb of the multialignment shown in was cut out and analyzed by Bootscan, using VK02 as query, window size 1,700 and step size 200. Five putative recombinant regions with VARV were identified. VK02 sequences between recombination breakpoints were extracted and realigned with several orthopoxviruses for phylogenetic analysis using either maximum likelihood or neighbor-joining models, as described. Blue boxes indicate the HPXV and HPXV-related cluster, and pink boxes indicate the VARV cluster. The position of VK02 in the trees is indicated by a red star. The numbers indicate bootstrap support of 1,000 replicates (>50% is shown). The scale bar indicates the number of substitutions per site.

Article Snippet: Putative recombination regions were analyzed using the Bootscan tool implemented in Simplot v.3.5.1 with the same parameters described above and the neighbor-joining tree model.

Techniques: Recombinant

Journal: mBio

Article Title: Gene duplication, gene loss, and recombination events with variola virus shaped the complex evolutionary path of historical American horsepox-based smallpox vaccines

doi: 10.1128/mbio.01887-23

Figure Lengend Snippet: Recombination in the variable region at the left end of the VK02 genome. ( A ) The multialignment of the variable region at the left end of the genomes of the six historical smallpox vaccines and HPXV_MNR-76 was scanned for percent similarity using Simplot, using the HPXV_MNR-76 sequence as query, window size 500, step size 50. Black arrows indicate the two regions of least similarity between VK02 and all other sequences, including HPXV_MNR-76. In one of the regions, in addition to VK02, MFDV_1902 also shares low similarity with the other viruses. ( B ) The multialignment included five variola virus strains and excluded all historical vaccines, except VK02 and VK08. Simplot was used with similar parameters, using VK02 as the query. Black arrows indicate regions 6A and 6B of least similarity between VK02 and both HPXV and VK08, and of highest similarity between VK02 and variola virus. ( C ) The first 4.5 kb of the multialignment shown in panel B was analyzed by Bootscan, using VK02 as query, window size 300, and step size 30. The two putative recombinant regions with VARV 6A and 6B are indicated. The VK02 sequences between recombination breakpoints were extracted and realigned with several orthopoxviruses for phylogenetic analysis using either maximum likelihood or neighbor-joining models. Blue boxes indicate the HPXV and HPXV-related cluster, and pink boxes indicate the VARV cluster. The position of VK02 in the trees is indicated by a red star. The numbers indicate the bootstrap support of 1,000 replicates (>50% is shown). The scale bar indicates the number of substitutions per site.

Article Snippet: Putative recombination regions were analyzed using the Bootscan tool implemented in Simplot v.3.5.1 with the same parameters described above and the neighbor-joining tree model.

Techniques: Vaccines, Sequencing, Virus, Recombinant

Journal: mBio

Article Title: Gene duplication, gene loss, and recombination events with variola virus shaped the complex evolutionary path of historical American horsepox-based smallpox vaccines

doi: 10.1128/mbio.01887-23

Figure Lengend Snippet: Schematic diagram of the VK02 genome. The yellow boxes represent the six VARV recombination regions in the VK02 genome that were detected by Bootscan analysis and supported by phylogenetic inference. Each region is zoomed in to show the genes involved in the recombination events (yellow arrows). The dotted lines on the arrows represent parts of the VK02 genes that are outside the area of recombination with VARV. Recombination subregions are indicated above the black lines, and gray areas indicate the bootstrap support by the phylogenetic analysis. Light gray, 60% < 70%; dark gray, >70%. Purple boxes indicate regions with CPXV genes in the VK02 genome.

Article Snippet: Putative recombination regions were analyzed using the Bootscan tool implemented in Simplot v.3.5.1 with the same parameters described above and the neighbor-joining tree model.

Techniques:

Journal: Frontiers in Microbiology

Article Title: Estimating HIV-1 Genetic Diversity in Brazil Through Next-Generation Sequencing

doi: 10.3389/fmicb.2019.00749

Figure Lengend Snippet: Different contigs representing HIV-1 sequences found in patient HI-17 through multiple infection investigation with their respective positions along the HXB2 reference genome and phylogenetic classification (A) considering the bootscaning (B) and maximum likelihood phylogenetic analyses. Each color represents a different subtype: red for subtype B, green for subtype F1 and blue for subtype C. Samples are identified before their respective virus structure and the HXB2 reference genome sequence is at the top of the Figure for reference positioning purpose.

Article Snippet: To investigate HIV-1 recombination the bootscaning tool of Simplot v.3.5.1 was used with the following parameters: window = 400 pb; steps = 40 pb; T/t = 2.0; gapstrip = on; replicas = 100; nucleotide substitution model = F84; method = Maximum Likelihood ( ).

Techniques: Infection, Virus, Sequencing