sequence identity matrix (Federation of European Neuroscience Societies)

Federation of European Neuroscience Societies sequence identity matrix
Sequence Identity Matrix, supplied by Federation of European Neuroscience Societies, used in various techniques. Bioz Stars score: 90/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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identity matrix diagram of aa sequence of rdrp domain (RStudio)

RStudio identity matrix diagram of aa sequence of rdrp domain

Diagrammatic sketch of the genome organization of SsEV11. ( A ) The information of Contig 2 obtained by virome sequencing and specific primers used for viral detection and rapid amplification of cDNA ends (RACE)-. The gray areas on both sides represent the RACE-OLOGO ligated using RACE method.Arrows represent direction and positions of the primers; F, F1 and F2 are primers ERV-F, ERV-F1 and ERV-F2; R, R1 and R2 are primers ERV-R, ERV-R1 and ERV-R2; Ra2 and Ra3 are primers Race2 and Race3. ( B ) The genome organization of SsEV11, showing 5′ and 3′ untranslated regions (UTR) and open reading flame (ORF) region. ( C ) The polyprotein encoded by the ORF of SsEV11 and its conserved function domains MTR, CRR, DEADc, Hel and <t>RdRp.</t> the Arabic numerals show the amino acid position of each conserved domain.

Identity Matrix Diagram Of Aa Sequence Of Rdrp Domain, supplied by RStudio, used in various techniques. Bioz Stars score: 90/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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multiple sequence alignment and identity/similarity matrix (MacVector inc)

MacVector inc multiple sequence alignment and identity/similarity matrix

Multiple Sequence Alignment And Identity/Similarity Matrix, supplied by MacVector inc, used in various techniques. Bioz Stars score: 90/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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nucleotide identity matrix (Bioedit Company)

Bioedit Company nucleotide identity matrix

Viral <t>nucleotide</t> loads in growth curve cultures. (A) The dynamic range and linearity of the CVA12 real-time assay. The threshold cycle (Ct) values (x-axis) were plotted against tenfold dilutions of CVA12. The parameters of the slope and y-intercept are given by the equation. R 2 , regression coefficient. (B) The levels of CVA12 RNA in the culture supernatants at 6, 12, 24, 48 and 72 hpi were determined by qRT-PCR ( n = 3 biological replicates). The 100 TCID 50 of CVA12 stock were used to infect RD and Hep-2 cell lines, respectively. (C) The levels of CVA12 RNA in the cell lysates at 6, 12, 24, 48 and 72 hpi were determined by qRT-PCR ( n = 3 biological replicates). The 100 TCID 50 of CVA12 stock were used to infect RD and Hep-2 cell lines, respectively. (D) Virus titer detection in RD and Hep-2 cell lines infected with 100 TCID 50 of CVA12 stock. The culture were collected at 6, 12, 24, 48 and 72 h post-infection (hpi). All the data are expressed as the mean ± SD of three biological replicates. Statistical significance was determined by ordinary one-way analysis of variance (ANOVA) with multiple comparisons methods using the GraphPad Prism software. * p < 0.05, ** p < 0.01, *** p < 0.001, **** p < 0.0001.

Nucleotide Identity Matrix, supplied by Bioedit Company, used in various techniques. Bioz Stars score: 86/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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Image Search Results

Journal: Viruses

Article Title: Genome Characterization and Phylogenetic Analysis of a Novel Endornavirus That Infects Fungal Pathogen Sclerotinia sclerotiorum

doi: 10.3390/v14030456

Figure Lengend Snippet: Diagrammatic sketch of the genome organization of SsEV11. ( A ) The information of Contig 2 obtained by virome sequencing and specific primers used for viral detection and rapid amplification of cDNA ends (RACE)-. The gray areas on both sides represent the RACE-OLOGO ligated using RACE method.Arrows represent direction and positions of the primers; F, F1 and F2 are primers ERV-F, ERV-F1 and ERV-F2; R, R1 and R2 are primers ERV-R, ERV-R1 and ERV-R2; Ra2 and Ra3 are primers Race2 and Race3. ( B ) The genome organization of SsEV11, showing 5′ and 3′ untranslated regions (UTR) and open reading flame (ORF) region. ( C ) The polyprotein encoded by the ORF of SsEV11 and its conserved function domains MTR, CRR, DEADc, Hel and RdRp. the Arabic numerals show the amino acid position of each conserved domain.

Article Snippet: Identity matrix diagram of aa sequence of RdRp domain was carried out online using Clustal Omega program ( https://www.ebi.ac.uk/Tools/msa/clustalo/ , accessed on 20 May 2021) and RStudio.

Techniques: Sequencing, Rapid Amplification of cDNA Ends

Alignment of RdRp domain of selected endornaviruses and endorna-like viruses. Conserved motifs are marked by Roman numerals from I to VIII. “Alpha” and “beta” represent alphaendornavirus and betaendornavirus, respectively; “Gamma” represents proposed gammaendornaviruses or endorna-like viruses. Novel endornavirus is highlighted with red characters.

Journal: Viruses

Article Title: Genome Characterization and Phylogenetic Analysis of a Novel Endornavirus That Infects Fungal Pathogen Sclerotinia sclerotiorum

doi: 10.3390/v14030456

Figure Lengend Snippet: Alignment of RdRp domain of selected endornaviruses and endorna-like viruses. Conserved motifs are marked by Roman numerals from I to VIII. “Alpha” and “beta” represent alphaendornavirus and betaendornavirus, respectively; “Gamma” represents proposed gammaendornaviruses or endorna-like viruses. Novel endornavirus is highlighted with red characters.

Techniques:

BLASTp analysis of polyprotein, RdRp, Hel, and Mtr domains between Sclerotinia sclerotiorum endornavirus 11 and selected endornaviruses.

Journal: Viruses

Article Title: Genome Characterization and Phylogenetic Analysis of a Novel Endornavirus That Infects Fungal Pathogen Sclerotinia sclerotiorum

doi: 10.3390/v14030456

Figure Lengend Snippet: BLASTp analysis of polyprotein, RdRp, Hel, and Mtr domains between Sclerotinia sclerotiorum endornavirus 11 and selected endornaviruses.

Techniques: Sequencing, Virus

Phylogenetic analysis of SsEV11 and other selected endornaviruses and endorna-like viruses based on the RdRP domain using Maximum Likelihood program with 1000 bootstrap replicates. GenBank accession numbers and virus names are listed in . Viruses written in blue are those infecting or associated with insects, written in red is newly identified virus.

Journal: Viruses

Article Title: Genome Characterization and Phylogenetic Analysis of a Novel Endornavirus That Infects Fungal Pathogen Sclerotinia sclerotiorum

doi: 10.3390/v14030456

Figure Lengend Snippet: Phylogenetic analysis of SsEV11 and other selected endornaviruses and endorna-like viruses based on the RdRP domain using Maximum Likelihood program with 1000 bootstrap replicates. GenBank accession numbers and virus names are listed in . Viruses written in blue are those infecting or associated with insects, written in red is newly identified virus.

Techniques: Virus

Matrix diagram of amino acid identities of RdRp domain among selected endornaviruses and endornalike viruses by using Clustal Omega 2.1. Alpha, Beta, and Gamma represent alphaendornaviruses, betaendornaviruses, and proposed gammaendornavirus, respectively; the cutoff values were 25%. The information of selected viruses and their RdRp domains are listed in . Viruses written in blue are viruses that infect insects. Newly identified endornavirus is written in red. Alignment analysis was carried out on website https://www.ebi.ac.uk/Tools/msa/clustalo/ , accessed on 20 May 2021.

Journal: Viruses

Article Title: Genome Characterization and Phylogenetic Analysis of a Novel Endornavirus That Infects Fungal Pathogen Sclerotinia sclerotiorum

doi: 10.3390/v14030456

Figure Lengend Snippet: Matrix diagram of amino acid identities of RdRp domain among selected endornaviruses and endornalike viruses by using Clustal Omega 2.1. Alpha, Beta, and Gamma represent alphaendornaviruses, betaendornaviruses, and proposed gammaendornavirus, respectively; the cutoff values were 25%. The information of selected viruses and their RdRp domains are listed in . Viruses written in blue are viruses that infect insects. Newly identified endornavirus is written in red. Alignment analysis was carried out on website https://www.ebi.ac.uk/Tools/msa/clustalo/ , accessed on 20 May 2021.

Techniques:

BLAST analysis of the RdRp domain of SsEV11 and selected endorna-like viruses.

Journal: Viruses

Article Title: Genome Characterization and Phylogenetic Analysis of a Novel Endornavirus That Infects Fungal Pathogen Sclerotinia sclerotiorum

doi: 10.3390/v14030456

Figure Lengend Snippet: BLAST analysis of the RdRp domain of SsEV11 and selected endorna-like viruses.

Techniques: Virus

Viral nucleotide loads in growth curve cultures. (A) The dynamic range and linearity of the CVA12 real-time assay. The threshold cycle (Ct) values (x-axis) were plotted against tenfold dilutions of CVA12. The parameters of the slope and y-intercept are given by the equation. R 2 , regression coefficient. (B) The levels of CVA12 RNA in the culture supernatants at 6, 12, 24, 48 and 72 hpi were determined by qRT-PCR ( n = 3 biological replicates). The 100 TCID 50 of CVA12 stock were used to infect RD and Hep-2 cell lines, respectively. (C) The levels of CVA12 RNA in the cell lysates at 6, 12, 24, 48 and 72 hpi were determined by qRT-PCR ( n = 3 biological replicates). The 100 TCID 50 of CVA12 stock were used to infect RD and Hep-2 cell lines, respectively. (D) Virus titer detection in RD and Hep-2 cell lines infected with 100 TCID 50 of CVA12 stock. The culture were collected at 6, 12, 24, 48 and 72 h post-infection (hpi). All the data are expressed as the mean ± SD of three biological replicates. Statistical significance was determined by ordinary one-way analysis of variance (ANOVA) with multiple comparisons methods using the GraphPad Prism software. * p < 0.05, ** p < 0.01, *** p < 0.001, **** p < 0.0001.

Journal: Frontiers in Microbiology

Article Title: The genetic and proliferation characterization analysis of novel coxsackievirus A12 in Beijing, China

doi: 10.3389/fmicb.2025.1665461

Figure Lengend Snippet: Viral nucleotide loads in growth curve cultures. (A) The dynamic range and linearity of the CVA12 real-time assay. The threshold cycle (Ct) values (x-axis) were plotted against tenfold dilutions of CVA12. The parameters of the slope and y-intercept are given by the equation. R 2 , regression coefficient. (B) The levels of CVA12 RNA in the culture supernatants at 6, 12, 24, 48 and 72 hpi were determined by qRT-PCR ( n = 3 biological replicates). The 100 TCID 50 of CVA12 stock were used to infect RD and Hep-2 cell lines, respectively. (C) The levels of CVA12 RNA in the cell lysates at 6, 12, 24, 48 and 72 hpi were determined by qRT-PCR ( n = 3 biological replicates). The 100 TCID 50 of CVA12 stock were used to infect RD and Hep-2 cell lines, respectively. (D) Virus titer detection in RD and Hep-2 cell lines infected with 100 TCID 50 of CVA12 stock. The culture were collected at 6, 12, 24, 48 and 72 h post-infection (hpi). All the data are expressed as the mean ± SD of three biological replicates. Statistical significance was determined by ordinary one-way analysis of variance (ANOVA) with multiple comparisons methods using the GraphPad Prism software. * p < 0.05, ** p < 0.01, *** p < 0.001, **** p < 0.0001.

Article Snippet: A nucleotide identity matrix was generated using BioEdit software.

Techniques: Quantitative RT-PCR, Virus, Infection, Software

The phylogenetic characteristics of CVA12. (A) Nucleotide distances between the different groups and within each group. (B) Principal components of CVA12 sequences with genogroups used as prior groups based on VP1 coding region. Different colors represent prior genogroups, and individual sequences are marked as dots. Results of eigenvalues analysis (PCA and DA) displayed in the inset. Axes represent the frst two principles. PCA, principal components analysis; DA, discriminant analysis. (C) Maximum likelihood phylogenetic tree based on the full-length VP1 coding region, with 1,000 bootstraps and SH-like approximate likelihood ratio tests (SH-aLRT) replicates at each node. The scale bar indicates nucleotide substitutions per site per year. The red colors represent the five CVA12 strains in this study.

Journal: Frontiers in Microbiology

Article Title: The genetic and proliferation characterization analysis of novel coxsackievirus A12 in Beijing, China

doi: 10.3389/fmicb.2025.1665461

Figure Lengend Snippet: The phylogenetic characteristics of CVA12. (A) Nucleotide distances between the different groups and within each group. (B) Principal components of CVA12 sequences with genogroups used as prior groups based on VP1 coding region. Different colors represent prior genogroups, and individual sequences are marked as dots. Results of eigenvalues analysis (PCA and DA) displayed in the inset. Axes represent the frst two principles. PCA, principal components analysis; DA, discriminant analysis. (C) Maximum likelihood phylogenetic tree based on the full-length VP1 coding region, with 1,000 bootstraps and SH-like approximate likelihood ratio tests (SH-aLRT) replicates at each node. The scale bar indicates nucleotide substitutions per site per year. The red colors represent the five CVA12 strains in this study.

Article Snippet: A nucleotide identity matrix was generated using BioEdit software.

Techniques:

sequence identity matrix function Search Results

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