Review




Structured Review

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

Software:

Article Title: Glucagon receptor inactivation leads to α-cell hyperplasia in zebrafish
Article Snippet: .. Phylogenetic analysis was performed by the neighborjoining method using the MEGA4 Software (The Biodesign Institute, Tempe, AZ, USA) and full-length amino acid sequences. ..

Article Title: Ror2 Receptor Mediates Wnt11 Ligand Signaling and Affects Convergence and Extension Movements in Zebrafish
Article Snippet: .. Phylogenetic trees were constructed using the neighbor-joining method with the MEGA4 software (The Biodesign Institute, Tempe, AZ) with the JTT model. Bootstrap analyses were run on 1000 replications. .. RT-PCR and Whole-mount in Situ Hybridization Total RNA was isolated from embryos using TRIzol reagent (Invitrogen).

Article Title: Ror2 Receptor Mediates Wnt11 Ligand Signaling and Affects Convergence and Extension Movements in Zebrafish
Article Snippet: .. Phylogenetic trees were constructed using the neighborjoining method with the MEGA4 software (The Biodesign Institute, Tempe, AZ) with the JTT model. Bootstrap analyses were run on 1000 replications. .. RT-PCR and Whole-mount in Situ Hybridization—Total RNA was isolated from embryos using TRIzol reagent (Invitrogen).

Article Title: Cloning, molecular characterization, and expression analysis of the signal transducer and activator of transcription 3 (STAT₃) gene from grass carp (Ctenopharyngodon idellus).
Article Snippet: Signal transducer and activator of transcription 3 (STAT3) binds to Janus kinase 2 (JAK2) to initiate the JAK2/STAT3 signal transduction pathway, which plays an important role in cancer cell proliferation, immune regulation, reproduction, lipid metabolism, and other physiological processes of the organism.. In this study, the cDNA sequence of the STAT3 gene from grass carp was cloned using RACE (rapidamplification of cDNA ends).. Twelve characteristics of the STAT3 gene and its encoded protein sequence were predicted and analyzed using bioinformatics methods; these features included the general physical and chemical properties, the hydrophobicity, the secondary structure and the three-dimensional structure of the protein.

Article Title: Design, Construction and Cloning of Truncated ORF2 and tPA sp -PADRE-Truncated ORF2 Gene Cassette From Hepatitis E Virus in the pVAX1 Expression Vector
Article Snippet: In order to confirm the sequence of the optimized gene in the expression recombinant plasmid pVAX-tPA sp -PADRE-truncated ORF2, sequencing of both strands with T7 forward and Bovine Growth Hormone (BGH) reverse primers was carried out (Bioneer, Korea). .. The result of the sequence analysis of the optimized gene using Mega4 software (Biodesign Institute, Tempe, AZ, USA) showed 100% concordance with the nucleotide sequence of the gene cassette in the initial recombinant pBMH-tPA sp -PADRE-truncated ORF2. .. After cloning of the truncated ORF2 PCR product (without PADRE and tPA sp sequences) in the pVAX1 vector, the recombinant plasmids were detected by colony PCR and restriction enzyme digestion with NheI and XhoI enzymes (New England BioLabs, USA) ( ).

Construct:

Article Title: Ror2 Receptor Mediates Wnt11 Ligand Signaling and Affects Convergence and Extension Movements in Zebrafish
Article Snippet: .. Phylogenetic trees were constructed using the neighbor-joining method with the MEGA4 software (The Biodesign Institute, Tempe, AZ) with the JTT model. Bootstrap analyses were run on 1000 replications. .. RT-PCR and Whole-mount in Situ Hybridization Total RNA was isolated from embryos using TRIzol reagent (Invitrogen).

Article Title: Ror2 Receptor Mediates Wnt11 Ligand Signaling and Affects Convergence and Extension Movements in Zebrafish
Article Snippet: .. Phylogenetic trees were constructed using the neighborjoining method with the MEGA4 software (The Biodesign Institute, Tempe, AZ) with the JTT model. Bootstrap analyses were run on 1000 replications. .. RT-PCR and Whole-mount in Situ Hybridization—Total RNA was isolated from embryos using TRIzol reagent (Invitrogen).

Article Title: Cloning, molecular characterization, and expression analysis of the signal transducer and activator of transcription 3 (STAT₃) gene from grass carp (Ctenopharyngodon idellus).
Article Snippet: Signal transducer and activator of transcription 3 (STAT3) binds to Janus kinase 2 (JAK2) to initiate the JAK2/STAT3 signal transduction pathway, which plays an important role in cancer cell proliferation, immune regulation, reproduction, lipid metabolism, and other physiological processes of the organism.. In this study, the cDNA sequence of the STAT3 gene from grass carp was cloned using RACE (rapidamplification of cDNA ends).. Twelve characteristics of the STAT3 gene and its encoded protein sequence were predicted and analyzed using bioinformatics methods; these features included the general physical and chemical properties, the hydrophobicity, the secondary structure and the three-dimensional structure of the protein.

other:

Article Title: Acquisition and persistence of antimicrobial-resistant bacteria isolated from dogs and cats admitted to a veterinary teaching hospital.
Article Snippet: U of antimicrobials in human or animal medicine is often followed by development of antimicrobial resistance.. The acquisition of infections among companion animals in a hospital or clinic setting is emerging as a public health threat that not only impacts an infected animal’s course of treatment and outcome but may substantially impact the health of humans (owners or veterinary staff) or other animals.. Like human patients in hospital settings, animals housed in VTHs are often susceptible to infection, and some bacteria typically found in dogs, such as Staphylococcus pseudintermedius, have the ability to carry and transfer resistance to a host of other pathogenic bacteria.

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
Article Snippet: The U3 sequences of the individual MDL-ERVs isolated from the C57BL/6J and Mus caroli/EiJ mice were surveyed for transcription regulatory elements using MatInspector (v.8.04) (Genomatix, Munich, Germany).

Sequencing:

Article Title: Design, Construction and Cloning of Truncated ORF2 and tPA sp -PADRE-Truncated ORF2 Gene Cassette From Hepatitis E Virus in the pVAX1 Expression Vector
Article Snippet: In order to confirm the sequence of the optimized gene in the expression recombinant plasmid pVAX-tPA sp -PADRE-truncated ORF2, sequencing of both strands with T7 forward and Bovine Growth Hormone (BGH) reverse primers was carried out (Bioneer, Korea). .. The result of the sequence analysis of the optimized gene using Mega4 software (Biodesign Institute, Tempe, AZ, USA) showed 100% concordance with the nucleotide sequence of the gene cassette in the initial recombinant pBMH-tPA sp -PADRE-truncated ORF2. .. After cloning of the truncated ORF2 PCR product (without PADRE and tPA sp sequences) in the pVAX1 vector, the recombinant plasmids were detected by colony PCR and restriction enzyme digestion with NheI and XhoI enzymes (New England BioLabs, USA) ( ).

Recombinant:

Article Title: Design, Construction and Cloning of Truncated ORF2 and tPA sp -PADRE-Truncated ORF2 Gene Cassette From Hepatitis E Virus in the pVAX1 Expression Vector
Article Snippet: In order to confirm the sequence of the optimized gene in the expression recombinant plasmid pVAX-tPA sp -PADRE-truncated ORF2, sequencing of both strands with T7 forward and Bovine Growth Hormone (BGH) reverse primers was carried out (Bioneer, Korea). .. The result of the sequence analysis of the optimized gene using Mega4 software (Biodesign Institute, Tempe, AZ, USA) showed 100% concordance with the nucleotide sequence of the gene cassette in the initial recombinant pBMH-tPA sp -PADRE-truncated ORF2. .. After cloning of the truncated ORF2 PCR product (without PADRE and tPA sp sequences) in the pVAX1 vector, the recombinant plasmids were detected by colony PCR and restriction enzyme digestion with NheI and XhoI enzymes (New England BioLabs, USA) ( ).



Similar Products

90
DNASTAR mega4 program
Mega4 Program, supplied by DNASTAR, 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/pm28457984-53-18-25
Average 90 stars, based on 1 article reviews
mega4 program - by Bioz Stars, 2026-11
90/100 stars
  Buy from Supplier

90
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
  Buy from Supplier

90
DNASTAR multiple alignment program mega4
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)]).
Multiple Alignment Program Mega4, supplied by DNASTAR, 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/pmc03550739-89-9-14
Average 90 stars, based on 1 article reviews
multiple alignment program mega4 - by Bioz Stars, 2026-11
90/100 stars
  Buy from Supplier

90
Amura Ltd program mega4
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)]).
Program Mega4, supplied by Amura Ltd, 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/program+mega4/pmc02644949-84-23-27
Average 90 stars, based on 1 article reviews
program mega4 - by Bioz Stars, 2026-11
90/100 stars
  Buy from Supplier

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: