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mega4 program  (Biodesign International Inc)

 
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    Biodesign International Inc mega4 program
    Patterns of nucleotide substitution: MDL-ERVs in cluster-B versus 157 MDL-ERVs of ~8–9 Kb in size Transition and transversion rates in the MDL-ERV proviral sequences were measured using <t> MEGA4. </t> Numbers in bold indicate transitional substitutions. Ts (transition), Tv (transversion), k (transition/transversion rate ratio). R represents overall transition/transversion bias, with A representing the number of adenosines, G the number of guanosines, T the number of thymidines, and C the number of cytidines. (R=[A*G*k purines +T*C*k pyrimidines ]/[(A+G)*(T+C)]).
    Mega4 Program, supplied by Biodesign International Inc, used in various techniques. Bioz Stars score: 90/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/product/program+mega4/mega+4+0/pmc03535300-109-23-28
    Average 90 stars, based on 1 article reviews
    mega4 program - by Bioz Stars, 2026-11
    90/100 stars

    Images

    1) Product Images from "Identification of a group of Mus dunni endogenous virus-like endogenous retroviruses from the C57BL/6J mouse genome: proviral genomes, strain distribution, expression characteristics, and genomic integration profile"

    Article Title: Identification of a group of Mus dunni endogenous virus-like endogenous retroviruses from the C57BL/6J mouse genome: proviral genomes, strain distribution, expression characteristics, and genomic integration profile

    Journal: Chromosome research : an international journal on the molecular, supramolecular and evolutionary aspects of chromosome biology

    doi: 10.1007/s10577-012-9322-z

    Patterns of nucleotide substitution: MDL-ERVs in cluster-B versus 157 MDL-ERVs of ~8–9 Kb in size Transition and transversion rates in the MDL-ERV proviral sequences were measured using MEGA4. Numbers in bold indicate transitional substitutions. Ts (transition), Tv (transversion), k (transition/transversion rate ratio). R represents overall transition/transversion bias, with A representing the number of adenosines, G the number of guanosines, T the number of thymidines, and C the number of cytidines. (R=[A*G*k purines +T*C*k pyrimidines ]/[(A+G)*(T+C)]).
    Figure Legend Snippet: Patterns of nucleotide substitution: MDL-ERVs in cluster-B versus 157 MDL-ERVs of ~8–9 Kb in size Transition and transversion rates in the MDL-ERV proviral sequences were measured using MEGA4. Numbers in bold indicate transitional substitutions. Ts (transition), Tv (transversion), k (transition/transversion rate ratio). R represents overall transition/transversion bias, with A representing the number of adenosines, G the number of guanosines, T the number of thymidines, and C the number of cytidines. (R=[A*G*k purines +T*C*k pyrimidines ]/[(A+G)*(T+C)]).

    Techniques Used:

    Related Articles

    other:

    Article Title: Identification and Characterization of Diplodia parva and Diplodia crataegicola Causing Black Rot of Chinese Quince
    Article Snippet: Sequence alignment and phylogenetic tree construction were performed using the DNA Star software (version 5.02, DNAStar Inc., Madison, WI, USA) and MEGA 4.0, respectively (Biodesign Institute, Tempe, AZ, USA).

    Article Title: Evaluation of Trichoderma atroviride and Trichoderma longibrachiatum as biocontrol agents in controlling red pepper anthracnose in Korea.
    Article Snippet: Sequence alignment and phylogenetic tree construction were performed using the DNASTAR software (Version 5.02, DNA Star Inc., Madison, USA) and MEGA 4.0, respectively (Biodesign Institute, Tempe, USA).

    Article Title: Mitochondrial DNA polymorphisms in Andersen-Tawil syndrome.
    Article Snippet: All the sequences obtained were aligned, and polymorphisms were identified using the DnaSP 5.10.1 (Universitat de Barcelona, Barcelona, Spain) and MEGA 4.0 (Center of Evolutionary Functional Genomics Biodesign Institute, Ar‐ izona State University, Arizona, United States) software.

    Article Title: Effects of Ensiling Oxytropis glabra with Whole-Plant Corn at Different Proportions on Fermentation Quality, Alkaloid Swainsonine Content, and Lactic Acid Bacteria Populations
    Article Snippet: The topologies of the trees were evaluated by bootstrap analysis of the sequence data using Molecular Evolutionary Genetic Analysis (MEGA) 4 software (The Biodesign Institute, Tempe, AZ, USA), based on random resampling with 1000 repetitions [ ].

    Article Title: Identification and Characterization of Xanthomonas arboricola pv. juglandis Causing Bacterial Blight of Walnuts in Korea
    Article Snippet: Sequence alignment and phylogenetic tree construction were performed using a DNA star program (version 5.02, DNA Star Inc., Madison, WI, USA) and MEGA 4.0 (Biodesign Institute, Tempe, AZ, USA).

    Article Title: Identification and Characterization of Xanthomonas arboricola pv. juglandis Causing Bacterial Blight of Walnuts in Korea
    Article Snippet: The distance dendrogram of the atpD , dnaK , efp , and rpoD gene sequences determined in this study was generated by the Mega 4.0 package (Biodesign Institute) according to the neighbor-joining method.

    Sequencing:

    Article Title: Monolaurin inhibits antibiotic-resistant Staphylococcus aureus in patients with atopic dermatitis.
    Article Snippet: .. The fusA sequences of fusidic acid-resistant S. aureus isolates were compared with the fusA sequence from S. aureus NCTC 8325 (GenBank accession no. NC_007795), using Mega 4 software (Biodesign Institute, Tempe, AZ, USA). .. The AutoDock v4.2 tool was used to perform a molecular docking simulation of fusidic acid with both wildtype EF-G and compared with mutated EF-G (mEF-G).

    Article Title: Monolaurin inhibits Antibiotic-resistant Staphylococcus aureus in Patients with Atopic Dermatitis
    Article Snippet: .. The fusA sequences of fusidic acid-resistant S. aureus isolates were compared with the fusA sequence from S. aureus NCTC 8325 (GenBank accession no. NC_007795), using Mega 4 software (Biodesign Institute, Tempe, AZ, USA). .. Molecular docking The AutoDock v4.2 tool was used to perform a molecular docking simulation of fusidic acid with both wild-type EF-G and compared with mutated EF-G (mEF-G).

    Software:

    Article Title: Monolaurin inhibits antibiotic-resistant Staphylococcus aureus in patients with atopic dermatitis.
    Article Snippet: .. The fusA sequences of fusidic acid-resistant S. aureus isolates were compared with the fusA sequence from S. aureus NCTC 8325 (GenBank accession no. NC_007795), using Mega 4 software (Biodesign Institute, Tempe, AZ, USA). .. The AutoDock v4.2 tool was used to perform a molecular docking simulation of fusidic acid with both wildtype EF-G and compared with mutated EF-G (mEF-G).

    Article Title: Monolaurin inhibits Antibiotic-resistant Staphylococcus aureus in Patients with Atopic Dermatitis
    Article Snippet: .. The fusA sequences of fusidic acid-resistant S. aureus isolates were compared with the fusA sequence from S. aureus NCTC 8325 (GenBank accession no. NC_007795), using Mega 4 software (Biodesign Institute, Tempe, AZ, USA). .. Molecular docking The AutoDock v4.2 tool was used to perform a molecular docking simulation of fusidic acid with both wild-type EF-G and compared with mutated EF-G (mEF-G).



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    Patterns of nucleotide substitution: MDL-ERVs in cluster-B versus 157 MDL-ERVs of ~8–9 Kb in size Transition and transversion rates in the MDL-ERV proviral sequences were measured using <t> MEGA4. </t> Numbers in bold indicate transitional substitutions. Ts (transition), Tv (transversion), k (transition/transversion rate ratio). R represents overall transition/transversion bias, with A representing the number of adenosines, G the number of guanosines, T the number of thymidines, and C the number of cytidines. (R=[A*G*k purines +T*C*k pyrimidines ]/[(A+G)*(T+C)]).
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    Patterns of nucleotide substitution: MDL-ERVs in cluster-B versus 157 MDL-ERVs of ~8–9 Kb in size Transition and transversion rates in the MDL-ERV proviral sequences were measured using <t> MEGA4. </t> Numbers in bold indicate transitional substitutions. Ts (transition), Tv (transversion), k (transition/transversion rate ratio). R represents overall transition/transversion bias, with A representing the number of adenosines, G the number of guanosines, T the number of thymidines, and C the number of cytidines. (R=[A*G*k purines +T*C*k pyrimidines ]/[(A+G)*(T+C)]).
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    Image Search Results


    Patterns of nucleotide substitution: MDL-ERVs in cluster-B versus 157 MDL-ERVs of ~8–9 Kb in size Transition and transversion rates in the MDL-ERV proviral sequences were measured using MEGA4. Numbers in bold indicate transitional substitutions. Ts (transition), Tv (transversion), k (transition/transversion rate ratio). R represents overall transition/transversion bias, with A representing the number of adenosines, G the number of guanosines, T the number of thymidines, and C the number of cytidines. (R=[A*G*k purines +T*C*k pyrimidines ]/[(A+G)*(T+C)]).

    Journal: Chromosome research : an international journal on the molecular, supramolecular and evolutionary aspects of chromosome biology

    Article Title: Identification of a group of Mus dunni endogenous virus-like endogenous retroviruses from the C57BL/6J mouse genome: proviral genomes, strain distribution, expression characteristics, and genomic integration profile

    doi: 10.1007/s10577-012-9322-z

    Figure Lengend Snippet: Patterns of nucleotide substitution: MDL-ERVs in cluster-B versus 157 MDL-ERVs of ~8–9 Kb in size Transition and transversion rates in the MDL-ERV proviral sequences were measured using MEGA4. Numbers in bold indicate transitional substitutions. Ts (transition), Tv (transversion), k (transition/transversion rate ratio). R represents overall transition/transversion bias, with A representing the number of adenosines, G the number of guanosines, T the number of thymidines, and C the number of cytidines. (R=[A*G*k purines +T*C*k pyrimidines ]/[(A+G)*(T+C)]).

    Article Snippet: Sequence diversity of two different MDL-ERV populations (cloned from the genomic DNAs of the C57BL/6J and Mus caroli/EiJ mice) was analyzed using the MEGA4 (Build 4028) program (The Biodesign Institute, Tempe, AZ) ( Tamura et al. 2007 ).

    Techniques: