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clustalw algorithm of codoncode aligner program  (CodonCode corporation)

 
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    CodonCode corporation clustalw algorithm of codoncode aligner program
    Clustalw Algorithm Of Codoncode Aligner Program, supplied by CodonCode corporation, 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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    Average 90 stars, based on 1 article reviews
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    Sequencing:

    Article Title: Mitochondrial Heteroplasmy and PCR Amplification Bias Lead to Wrong Species Delimitation with High Confidence in the South American and Antarctic Marine Bivalve Aequiyoldia eightsii Species Complex.
    Article Snippet: All PCR products were sequenced for both strands by Eurofins Genomics GmbH (Ebersberg, Germany) using the same primers that were utilized during amplification. .. COI, histone H3, and 18S sequences were aligned using the ClustalW algorithm of CodonCode Aligner program (version 5.1.5; CodonCode Corporation, Dedham, MA, USA), and all chromatograms were inspected visually for sequencing mistakes. .. For COI, a haplotype network was constructed using the Neighbor-Joining algorithm and implementing the Hasegawa–Kishino–Yano (HKY) model of substitution in Geneious using default parameters (version 8.1.9, Biomatters Ltd., Auckland, New Zealand) and Haplotype Viewer (Center of Integrative Bioinformatics Vienna, http://www.cibiv.at (accessed on 6 April 2022)).

    Article Title: Mitochondrial Heteroplasmy and PCR Amplification Bias Lead to Wrong Species Delimitation with High Confidence in the South American and Antarctic Marine Bivalve Aequiyoldia eightsii Species Complex
    Article Snippet: All PCR products were sequenced for both strands by Eurofins Genomics GmbH (Ebersberg, Germany) using the same primers that were utilized during amplification. .. COI , histone H3 , and 18S sequences were aligned using the ClustalW algorithm of CodonCode Aligner program (version 5.1.5; CodonCode Corporation, Dedham, MA, USA), and all chromatograms were inspected visually for sequencing mistakes. .. For COI , a haplotype network was constructed using the Neighbor-Joining algorithm and implementing the Hasegawa–Kishino–Yano (HKY) model of substitution in Geneious using default parameters (version 8.1.9, Biomatters Ltd., Auckland, New Zealand) and Haplotype Viewer (Center of Integrative Bioinformatics Vienna, http://www.cibiv.at (accessed on 6 April 2022)).

    other:

    Article Title: Unrevealing the leaf frogs Cerrado diversity: A new species of Pithecopus (Anura, Arboranae, Phyllomedusidae) from the Mato Grosso state, Brazil
    Article Snippet: We aligned sequences using CLUSTALW [ ] implemented in CodonCode Aligner 4.0.



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    Fig. 1. Molecular characterization of CPB proteasome subunit beta type-5 (CPB-PSMB5). (A) Prediction of signature motifs and alignment of nucleotide sequences of CPB-PSMB5 with other four well-known insect and potato plant PSMB5. Sequence alignment used Clustal W program of <t>MegAlign</t> (DNASTAR, Version 7.0). Species acronyms and GenBank accession numbers of PSMB5 amino acids are listed in Table S1. (B) Predicted three-dimensional structure of CPB-PSMB5 showing key structural domains. Alpha-helices and beta-sheets are depicted in the model as cyan, and yellow, respectively. The beta subunit interaction site domain is highlighted in brown. Green regions represent the active site. (C) Phylogenetic tree of CPB-PSMB5 (highlighted in a red rounded rectangle) and other PSMB5 sequences from different insect orders. The tree was generated with MEGA 7 using Neighbor-joining method. Bootstrap values on nodes were obtained with 1000 replicates. GenBank accession numbers are provided in Supplementary Table S1. (For interpretation of the references to color in this figure legend, the reader is referred to the web version of this article.)
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    Fig. 1. Molecular characterization of CPB proteasome subunit beta type-5 (CPB-PSMB5). (A) Prediction of signature motifs and alignment of nucleotide sequences of CPB-PSMB5 with other four well-known insect and potato plant PSMB5. Sequence alignment used Clustal W program of <t>MegAlign</t> (DNASTAR, Version 7.0). Species acronyms and GenBank accession numbers of PSMB5 amino acids are listed in Table S1. (B) Predicted three-dimensional structure of CPB-PSMB5 showing key structural domains. Alpha-helices and beta-sheets are depicted in the model as cyan, and yellow, respectively. The beta subunit interaction site domain is highlighted in brown. Green regions represent the active site. (C) Phylogenetic tree of CPB-PSMB5 (highlighted in a red rounded rectangle) and other PSMB5 sequences from different insect orders. The tree was generated with MEGA 7 using Neighbor-joining method. Bootstrap values on nodes were obtained with 1000 replicates. GenBank accession numbers are provided in Supplementary Table S1. (For interpretation of the references to color in this figure legend, the reader is referred to the web version of this article.)
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    Fig. 1. Molecular characterization of CPB proteasome subunit beta type-5 (CPB-PSMB5). (A) Prediction of signature motifs and alignment of nucleotide sequences of CPB-PSMB5 with other four well-known insect and potato plant PSMB5. Sequence alignment used Clustal W program of MegAlign (DNASTAR, Version 7.0). Species acronyms and GenBank accession numbers of PSMB5 amino acids are listed in Table S1. (B) Predicted three-dimensional structure of CPB-PSMB5 showing key structural domains. Alpha-helices and beta-sheets are depicted in the model as cyan, and yellow, respectively. The beta subunit interaction site domain is highlighted in brown. Green regions represent the active site. (C) Phylogenetic tree of CPB-PSMB5 (highlighted in a red rounded rectangle) and other PSMB5 sequences from different insect orders. The tree was generated with MEGA 7 using Neighbor-joining method. Bootstrap values on nodes were obtained with 1000 replicates. GenBank accession numbers are provided in Supplementary Table S1. (For interpretation of the references to color in this figure legend, the reader is referred to the web version of this article.)

    Journal: Pesticide Biochemistry and Physiology

    Article Title: Development and efficacy of dsRNA pesticides targeting the Colorado potato beetle with enhanced stability via chitosan formulations

    doi: 10.1016/j.pestbp.2025.106606

    Figure Lengend Snippet: Fig. 1. Molecular characterization of CPB proteasome subunit beta type-5 (CPB-PSMB5). (A) Prediction of signature motifs and alignment of nucleotide sequences of CPB-PSMB5 with other four well-known insect and potato plant PSMB5. Sequence alignment used Clustal W program of MegAlign (DNASTAR, Version 7.0). Species acronyms and GenBank accession numbers of PSMB5 amino acids are listed in Table S1. (B) Predicted three-dimensional structure of CPB-PSMB5 showing key structural domains. Alpha-helices and beta-sheets are depicted in the model as cyan, and yellow, respectively. The beta subunit interaction site domain is highlighted in brown. Green regions represent the active site. (C) Phylogenetic tree of CPB-PSMB5 (highlighted in a red rounded rectangle) and other PSMB5 sequences from different insect orders. The tree was generated with MEGA 7 using Neighbor-joining method. Bootstrap values on nodes were obtained with 1000 replicates. GenBank accession numbers are provided in Supplementary Table S1. (For interpretation of the references to color in this figure legend, the reader is referred to the web version of this article.)

    Article Snippet: Sequence alignment was performed using the Clustal W program within MegAlign (DNASTAR, Version 7.0).

    Techniques: Sequencing, Generated