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  • 88
    Bioedit Company clustalw multiple alignment tool
    Conserved architecture of the C-terminal catalytic region of Mitrecin A as compared to other similar carboxypeptidases. C-termini of sequences with similarity to Mitrecin A ( Fig. 1 ), identified in MEROPS Blast searches, were aligned against the Mitrecin A C-terminus using the <t>clustalw</t> multiple alignment tool. Conserved amino acid residues and motifs within the C-terminal M15 peptidase subfamily domains as aligned against Mitrecin A are shaded in light blue. Conserved region 1 (CR1), conserved region 2 (CR2), and conserved region 3 (CR3) are indicated. Histidine (H) and aspartic acid (D) residues, inferred by analysis in MEROPS to be necessary for interaction with the metal ion of the catalytic site binding pocket, are enclosed in boxes. The active site residue is shaded in dark blue.
    Clustalw Multiple Alignment Tool, supplied by Bioedit Company, used in various techniques. Bioz Stars score: 88/100, based on 76 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    SourceForge net burrows wheeler alignment tool
    Conserved architecture of the C-terminal catalytic region of Mitrecin A as compared to other similar carboxypeptidases. C-termini of sequences with similarity to Mitrecin A ( Fig. 1 ), identified in MEROPS Blast searches, were aligned against the Mitrecin A C-terminus using the <t>clustalw</t> multiple alignment tool. Conserved amino acid residues and motifs within the C-terminal M15 peptidase subfamily domains as aligned against Mitrecin A are shaded in light blue. Conserved region 1 (CR1), conserved region 2 (CR2), and conserved region 3 (CR3) are indicated. Histidine (H) and aspartic acid (D) residues, inferred by analysis in MEROPS to be necessary for interaction with the metal ion of the catalytic site binding pocket, are enclosed in boxes. The active site residue is shaded in dark blue.
    Burrows Wheeler Alignment Tool, supplied by SourceForge net, used in various techniques. Bioz Stars score: 88/100, based on 58 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Applied Precision Inc softworx alignment tool
    Conserved architecture of the C-terminal catalytic region of Mitrecin A as compared to other similar carboxypeptidases. C-termini of sequences with similarity to Mitrecin A ( Fig. 1 ), identified in MEROPS Blast searches, were aligned against the Mitrecin A C-terminus using the <t>clustalw</t> multiple alignment tool. Conserved amino acid residues and motifs within the C-terminal M15 peptidase subfamily domains as aligned against Mitrecin A are shaded in light blue. Conserved region 1 (CR1), conserved region 2 (CR2), and conserved region 3 (CR3) are indicated. Histidine (H) and aspartic acid (D) residues, inferred by analysis in MEROPS to be necessary for interaction with the metal ion of the catalytic site binding pocket, are enclosed in boxes. The active site residue is shaded in dark blue.
    Softworx Alignment Tool, supplied by Applied Precision Inc, used in various techniques. Bioz Stars score: 88/100, based on 56 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    88
    Biotechnology Information local alignment search tool blast
    Conserved architecture of the C-terminal catalytic region of Mitrecin A as compared to other similar carboxypeptidases. C-termini of sequences with similarity to Mitrecin A ( Fig. 1 ), identified in MEROPS Blast searches, were aligned against the Mitrecin A C-terminus using the <t>clustalw</t> multiple alignment tool. Conserved amino acid residues and motifs within the C-terminal M15 peptidase subfamily domains as aligned against Mitrecin A are shaded in light blue. Conserved region 1 (CR1), conserved region 2 (CR2), and conserved region 3 (CR3) are indicated. Histidine (H) and aspartic acid (D) residues, inferred by analysis in MEROPS to be necessary for interaction with the metal ion of the catalytic site binding pocket, are enclosed in boxes. The active site residue is shaded in dark blue.
    Local Alignment Search Tool Blast, supplied by Biotechnology Information, used in various techniques. Bioz Stars score: 88/100, based on 72 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    88
    MacVector clustalw alignment tool
    Conserved architecture of the C-terminal catalytic region of Mitrecin A as compared to other similar carboxypeptidases. C-termini of sequences with similarity to Mitrecin A ( Fig. 1 ), identified in MEROPS Blast searches, were aligned against the Mitrecin A C-terminus using the <t>clustalw</t> multiple alignment tool. Conserved amino acid residues and motifs within the C-terminal M15 peptidase subfamily domains as aligned against Mitrecin A are shaded in light blue. Conserved region 1 (CR1), conserved region 2 (CR2), and conserved region 3 (CR3) are indicated. Histidine (H) and aspartic acid (D) residues, inferred by analysis in MEROPS to be necessary for interaction with the metal ion of the catalytic site binding pocket, are enclosed in boxes. The active site residue is shaded in dark blue.
    Clustalw Alignment Tool, supplied by MacVector, used in various techniques. Bioz Stars score: 88/100, based on 56 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    90
    Biomatters Ltd geneious alignment tool
    (A) Bayesian phylogenetic tree of the H gene nucleotide alignment from tigers Pt2004 and Pt2010-3 and representative CDV sequences obtained from GenBank. Sequences were aligned using <t>Geneious</t> Pro software. Bayesian posterior probabilities of branching demonstrate the robustness of the individual groups. (B) Distance matrix analysis of CDV H gene sequences. Pairwise identities of nucleotide and amino acid sequences (boldface) between different strains of CDV were obtained through GenBank and generated from a pairwise distance matrix calculated using PAUP software.
    Geneious Alignment Tool, supplied by Biomatters Ltd, used in various techniques. Bioz Stars score: 90/100, based on 54 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    88
    Biotechnology Information alignment search tool
    (A) Bayesian phylogenetic tree of the H gene nucleotide alignment from tigers Pt2004 and Pt2010-3 and representative CDV sequences obtained from GenBank. Sequences were aligned using <t>Geneious</t> Pro software. Bayesian posterior probabilities of branching demonstrate the robustness of the individual groups. (B) Distance matrix analysis of CDV H gene sequences. Pairwise identities of nucleotide and amino acid sequences (boldface) between different strains of CDV were obtained through GenBank and generated from a pairwise distance matrix calculated using PAUP software.
    Alignment Search Tool, supplied by Biotechnology Information, used in various techniques. Bioz Stars score: 88/100, based on 44 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    85
    Bioedit Company clustal w multiple sequence alignment tool
    (A) Bayesian phylogenetic tree of the H gene nucleotide alignment from tigers Pt2004 and Pt2010-3 and representative CDV sequences obtained from GenBank. Sequences were aligned using <t>Geneious</t> Pro software. Bayesian posterior probabilities of branching demonstrate the robustness of the individual groups. (B) Distance matrix analysis of CDV H gene sequences. Pairwise identities of nucleotide and amino acid sequences (boldface) between different strains of CDV were obtained through GenBank and generated from a pairwise distance matrix calculated using PAUP software.
    Clustal W Multiple Sequence Alignment Tool, supplied by Bioedit Company, used in various techniques. Bioz Stars score: 85/100, based on 33 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    92
    Ebiox ebiox alignment tool
    (A) Bayesian phylogenetic tree of the H gene nucleotide alignment from tigers Pt2004 and Pt2010-3 and representative CDV sequences obtained from GenBank. Sequences were aligned using <t>Geneious</t> Pro software. Bayesian posterior probabilities of branching demonstrate the robustness of the individual groups. (B) Distance matrix analysis of CDV H gene sequences. Pairwise identities of nucleotide and amino acid sequences (boldface) between different strains of CDV were obtained through GenBank and generated from a pairwise distance matrix calculated using PAUP software.
    Ebiox Alignment Tool, supplied by Ebiox, used in various techniques. Bioz Stars score: 92/100, based on 4 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    88
    Santa Cruz Biotechnology blast like alignment tool
    (A) Bayesian phylogenetic tree of the H gene nucleotide alignment from tigers Pt2004 and Pt2010-3 and representative CDV sequences obtained from GenBank. Sequences were aligned using <t>Geneious</t> Pro software. Bayesian posterior probabilities of branching demonstrate the robustness of the individual groups. (B) Distance matrix analysis of CDV H gene sequences. Pairwise identities of nucleotide and amino acid sequences (boldface) between different strains of CDV were obtained through GenBank and generated from a pairwise distance matrix calculated using PAUP software.
    Blast Like Alignment Tool, supplied by Santa Cruz Biotechnology, used in various techniques. Bioz Stars score: 88/100, based on 5 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    85
    Biotechnology Information basic local alignment search tool nucleotide
    (A) Bayesian phylogenetic tree of the H gene nucleotide alignment from tigers Pt2004 and Pt2010-3 and representative CDV sequences obtained from GenBank. Sequences were aligned using <t>Geneious</t> Pro software. Bayesian posterior probabilities of branching demonstrate the robustness of the individual groups. (B) Distance matrix analysis of CDV H gene sequences. Pairwise identities of nucleotide and amino acid sequences (boldface) between different strains of CDV were obtained through GenBank and generated from a pairwise distance matrix calculated using PAUP software.
    Basic Local Alignment Search Tool Nucleotide, supplied by Biotechnology Information, used in various techniques. Bioz Stars score: 85/100, based on 12 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    91
    SourceForge net burrows wheeler aligner tool
    (A) Bayesian phylogenetic tree of the H gene nucleotide alignment from tigers Pt2004 and Pt2010-3 and representative CDV sequences obtained from GenBank. Sequences were aligned using <t>Geneious</t> Pro software. Bayesian posterior probabilities of branching demonstrate the robustness of the individual groups. (B) Distance matrix analysis of CDV H gene sequences. Pairwise identities of nucleotide and amino acid sequences (boldface) between different strains of CDV were obtained through GenBank and generated from a pairwise distance matrix calculated using PAUP software.
    Burrows Wheeler Aligner Tool, supplied by SourceForge net, used in various techniques. Bioz Stars score: 91/100, based on 9 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    90
    Biotechnology Information local alignment search tool blastx
    (A) Bayesian phylogenetic tree of the H gene nucleotide alignment from tigers Pt2004 and Pt2010-3 and representative CDV sequences obtained from GenBank. Sequences were aligned using <t>Geneious</t> Pro software. Bayesian posterior probabilities of branching demonstrate the robustness of the individual groups. (B) Distance matrix analysis of CDV H gene sequences. Pairwise identities of nucleotide and amino acid sequences (boldface) between different strains of CDV were obtained through GenBank and generated from a pairwise distance matrix calculated using PAUP software.
    Local Alignment Search Tool Blastx, supplied by Biotechnology Information, used in various techniques. Bioz Stars score: 90/100, based on 17 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    85
    Biotechnology Information nucleotide basic local alignment search tool blastn
    (A) Bayesian phylogenetic tree of the H gene nucleotide alignment from tigers Pt2004 and Pt2010-3 and representative CDV sequences obtained from GenBank. Sequences were aligned using <t>Geneious</t> Pro software. Bayesian posterior probabilities of branching demonstrate the robustness of the individual groups. (B) Distance matrix analysis of CDV H gene sequences. Pairwise identities of nucleotide and amino acid sequences (boldface) between different strains of CDV were obtained through GenBank and generated from a pairwise distance matrix calculated using PAUP software.
    Nucleotide Basic Local Alignment Search Tool Blastn, supplied by Biotechnology Information, used in various techniques. Bioz Stars score: 85/100, based on 17 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    93
    CLC Bio align contigs tool
    Species distribution of Litsea acuminata <t>contigs</t> BLAST searched against 14 plant species in the Plant Database.
    Align Contigs Tool, supplied by CLC Bio, used in various techniques. Bioz Stars score: 93/100, based on 9 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    SourceForge net alignment tool bwa
    Species distribution of Litsea acuminata <t>contigs</t> BLAST searched against 14 plant species in the Plant Database.
    Alignment Tool Bwa, supplied by SourceForge net, used in various techniques. Bioz Stars score: 90/100, based on 10 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Carna alignment tool locarna
    Species distribution of Litsea acuminata <t>contigs</t> BLAST searched against 14 plant species in the Plant Database.
    Alignment Tool Locarna, supplied by Carna, used in various techniques. Bioz Stars score: 92/100, based on 2 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Bioedit Company alignment tools bioedit 7 0 0
    Species distribution of Litsea acuminata <t>contigs</t> BLAST searched against 14 plant species in the Plant Database.
    Alignment Tools Bioedit 7 0 0, supplied by Bioedit Company, used in various techniques. Bioz Stars score: 92/100, based on 2 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    85
    Biotechnology Information basic local alignment sequence tool blast algorithm
    Species distribution of Litsea acuminata <t>contigs</t> BLAST searched against 14 plant species in the Plant Database.
    Basic Local Alignment Sequence Tool Blast Algorithm, supplied by Biotechnology Information, used in various techniques. Bioz Stars score: 85/100, based on 9 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    93
    Bioedit Company bioedit alignment tools
    Sequences of the β-PV isoforms of Gadus morhua and Scomber japonicus . (a) Sequence alignment generated using <t>BioEdit</t> tools and their amino acid color table . (b) Pairwise identity calculated using BioEdit tools . (c) Relevant regions for PARV19 and serum IgE binding. The PARV19 epitope (orange rectangle) was predicted to include residues 13-39 36 . The displayed IgE binding epitopes (red rectangles) were determined using gmPV1-templated dodecapeptides 25 . (d) Segments involved in the globular and amyloid folds of β-PV. The globular fold contains three helix-loop-helix (AB, CD and EF) EF-hands, of which only CD and EF bind cations 3 , 4 , 26 , 43 . Regions assembling into amyloids were predicted by AmylPred2, and they are depicted by arrows. Regions known to form amyloids in gmPV1 are depicted with pink arrows 25 , 30 .
    Bioedit Alignment Tools, supplied by Bioedit Company, used in various techniques. Bioz Stars score: 93/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Image Search Results


    Conserved architecture of the C-terminal catalytic region of Mitrecin A as compared to other similar carboxypeptidases. C-termini of sequences with similarity to Mitrecin A ( Fig. 1 ), identified in MEROPS Blast searches, were aligned against the Mitrecin A C-terminus using the clustalw multiple alignment tool. Conserved amino acid residues and motifs within the C-terminal M15 peptidase subfamily domains as aligned against Mitrecin A are shaded in light blue. Conserved region 1 (CR1), conserved region 2 (CR2), and conserved region 3 (CR3) are indicated. Histidine (H) and aspartic acid (D) residues, inferred by analysis in MEROPS to be necessary for interaction with the metal ion of the catalytic site binding pocket, are enclosed in boxes. The active site residue is shaded in dark blue.

    Journal: Letters in Applied Microbiology

    Article Title: Mitrecin A, an endolysin-like bacteriolytic enzyme from a newly isolated soil streptomycete

    doi: 10.1111/lam.12220

    Figure Lengend Snippet: Conserved architecture of the C-terminal catalytic region of Mitrecin A as compared to other similar carboxypeptidases. C-termini of sequences with similarity to Mitrecin A ( Fig. 1 ), identified in MEROPS Blast searches, were aligned against the Mitrecin A C-terminus using the clustalw multiple alignment tool. Conserved amino acid residues and motifs within the C-terminal M15 peptidase subfamily domains as aligned against Mitrecin A are shaded in light blue. Conserved region 1 (CR1), conserved region 2 (CR2), and conserved region 3 (CR3) are indicated. Histidine (H) and aspartic acid (D) residues, inferred by analysis in MEROPS to be necessary for interaction with the metal ion of the catalytic site binding pocket, are enclosed in boxes. The active site residue is shaded in dark blue.

    Article Snippet: Protein sequences with high similarity to Mitrecin A identified within the database searches were aligned against the Mitrecin A protein sequence using the clustalw multiple alignment tool (Thompson et al . ) within BioEdit biological sequence alignment editor, ver.

    Techniques: Binding Assay

    (A) Bayesian phylogenetic tree of the H gene nucleotide alignment from tigers Pt2004 and Pt2010-3 and representative CDV sequences obtained from GenBank. Sequences were aligned using Geneious Pro software. Bayesian posterior probabilities of branching demonstrate the robustness of the individual groups. (B) Distance matrix analysis of CDV H gene sequences. Pairwise identities of nucleotide and amino acid sequences (boldface) between different strains of CDV were obtained through GenBank and generated from a pairwise distance matrix calculated using PAUP software.

    Journal: mBio

    Article Title: Canine Distemper Virus: an Emerging Disease in Wild Endangered Amur Tigers (Panthera tigris altaica)

    doi: 10.1128/mBio.00410-13

    Figure Lengend Snippet: (A) Bayesian phylogenetic tree of the H gene nucleotide alignment from tigers Pt2004 and Pt2010-3 and representative CDV sequences obtained from GenBank. Sequences were aligned using Geneious Pro software. Bayesian posterior probabilities of branching demonstrate the robustness of the individual groups. (B) Distance matrix analysis of CDV H gene sequences. Pairwise identities of nucleotide and amino acid sequences (boldface) between different strains of CDV were obtained through GenBank and generated from a pairwise distance matrix calculated using PAUP software.

    Article Snippet: The nucleotide sequences of the H gene were translated and aligned using the Geneious alignment tool (Geneious Pro 5.1.7 software; Biomatters Ltd., Auckland, New Zealand) and analyzed for amino acid polymorphisms at positions 530 and 549 in the SLAM receptor binding region of the H gene.

    Techniques: Software, Generated

    Species distribution of Litsea acuminata contigs BLAST searched against 14 plant species in the Plant Database.

    Journal: PLoS ONE

    Article Title: Transcriptome profile of cup-shaped galls in Litsea acuminata leaves

    doi: 10.1371/journal.pone.0205265

    Figure Lengend Snippet: Species distribution of Litsea acuminata contigs BLAST searched against 14 plant species in the Plant Database.

    Article Snippet: Genes were aligned using CLC bio’s Align Contigs tool to find unique and shared genes between gall tissue and host leaves.

    Techniques:

    Venn plot displaying amount of shared and specific genes in gall tissue and the host leaf. Genes were the de novo assembled contigs after BLAST in Plant Database.

    Journal: PLoS ONE

    Article Title: Transcriptome profile of cup-shaped galls in Litsea acuminata leaves

    doi: 10.1371/journal.pone.0205265

    Figure Lengend Snippet: Venn plot displaying amount of shared and specific genes in gall tissue and the host leaf. Genes were the de novo assembled contigs after BLAST in Plant Database.

    Article Snippet: Genes were aligned using CLC bio’s Align Contigs tool to find unique and shared genes between gall tissue and host leaves.

    Techniques:

    Sequences of the β-PV isoforms of Gadus morhua and Scomber japonicus . (a) Sequence alignment generated using BioEdit tools and their amino acid color table . (b) Pairwise identity calculated using BioEdit tools . (c) Relevant regions for PARV19 and serum IgE binding. The PARV19 epitope (orange rectangle) was predicted to include residues 13-39 36 . The displayed IgE binding epitopes (red rectangles) were determined using gmPV1-templated dodecapeptides 25 . (d) Segments involved in the globular and amyloid folds of β-PV. The globular fold contains three helix-loop-helix (AB, CD and EF) EF-hands, of which only CD and EF bind cations 3 , 4 , 26 , 43 . Regions assembling into amyloids were predicted by AmylPred2, and they are depicted by arrows. Regions known to form amyloids in gmPV1 are depicted with pink arrows 25 , 30 .

    Journal: bioRxiv

    Article Title: Reconstruction of fish allergenicity from the content and structural traits of the component β-parvalbumin isoforms

    doi: 10.1101/813659

    Figure Lengend Snippet: Sequences of the β-PV isoforms of Gadus morhua and Scomber japonicus . (a) Sequence alignment generated using BioEdit tools and their amino acid color table . (b) Pairwise identity calculated using BioEdit tools . (c) Relevant regions for PARV19 and serum IgE binding. The PARV19 epitope (orange rectangle) was predicted to include residues 13-39 36 . The displayed IgE binding epitopes (red rectangles) were determined using gmPV1-templated dodecapeptides 25 . (d) Segments involved in the globular and amyloid folds of β-PV. The globular fold contains three helix-loop-helix (AB, CD and EF) EF-hands, of which only CD and EF bind cations 3 , 4 , 26 , 43 . Regions assembling into amyloids were predicted by AmylPred2, and they are depicted by arrows. Regions known to form amyloids in gmPV1 are depicted with pink arrows 25 , 30 .

    Article Snippet: Analysis with BioEdit alignment tools showed 56% global identity and 86% global homology among the isoforms.

    Techniques: Sequencing, Generated, Binding Assay