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  • 99
    Thermo Fisher vector nti
    Dot Martrix analyses of the whole MuLV-1313 genome . Dot plots of the MuLV-1313 genome (GenBank accession number AF411814 ) were constructed utilizing the COMPARE which produced files of 15621 points of full-length MuLV genomes. Dot matrix was constructed using DOTPLOT programs of the Wisconsin Package, Version 9.0, Genetics Computer Group (GCG), Madison WI and Vector <t>NTI</t> (Invitrogen, <t>Carlsbad,</t> California) tool with windows setting at 21 and stringency at 44. This analysis compares each nucleotide position with the corresponding position of another genome (Dot). Solid diagonal line represents similarity and broken lines indicate gaps. Although Dot-Matrix analyses were performed on several MuLV strains, viruses that showed high similarity scores are shown in panels A, B and C (see Additional File 2). Dot Matrix analyses of full-length genomic sequences shown include ; Panel A, Cas-Br-E [25] (X57540); Panel B, AKV (J01998), and Panel C, Moloney (J02255). The highest nucleotide similarity is observed with the CAS-Br-E ecotropic virus isolated from a Southern California Wild mouse with paralysis (Panel A). This is followed by Moloney [8] and AKV MuLV strains [85] (Panels B C respectively) . Note, the env sequences of MuLV-1313 are totally unrelated to all three viruses shown by large gap in this area of the diagonal line. In addition, note the numerous broken lines in gag and pol regions of the Moloney and AKV MuLV genomes.
    Vector Nti, supplied by Thermo Fisher, used in various techniques. Bioz Stars score: 99/100, based on 3938 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Thermo Fisher vector nti advance 10
    Dot Martrix analyses of the whole MuLV-1313 genome . Dot plots of the MuLV-1313 genome (GenBank accession number AF411814 ) were constructed utilizing the COMPARE which produced files of 15621 points of full-length MuLV genomes. Dot matrix was constructed using DOTPLOT programs of the Wisconsin Package, Version 9.0, Genetics Computer Group (GCG), Madison WI and Vector <t>NTI</t> (Invitrogen, <t>Carlsbad,</t> California) tool with windows setting at 21 and stringency at 44. This analysis compares each nucleotide position with the corresponding position of another genome (Dot). Solid diagonal line represents similarity and broken lines indicate gaps. Although Dot-Matrix analyses were performed on several MuLV strains, viruses that showed high similarity scores are shown in panels A, B and C (see Additional File 2). Dot Matrix analyses of full-length genomic sequences shown include ; Panel A, Cas-Br-E [25] (X57540); Panel B, AKV (J01998), and Panel C, Moloney (J02255). The highest nucleotide similarity is observed with the CAS-Br-E ecotropic virus isolated from a Southern California Wild mouse with paralysis (Panel A). This is followed by Moloney [8] and AKV MuLV strains [85] (Panels B C respectively) . Note, the env sequences of MuLV-1313 are totally unrelated to all three viruses shown by large gap in this area of the diagonal line. In addition, note the numerous broken lines in gag and pol regions of the Moloney and AKV MuLV genomes.
    Vector Nti Advance 10, supplied by Thermo Fisher, used in various techniques. Bioz Stars score: 91/100, based on 566 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Thermo Fisher vector nti advance
    Dot Martrix analyses of the whole MuLV-1313 genome . Dot plots of the MuLV-1313 genome (GenBank accession number AF411814 ) were constructed utilizing the COMPARE which produced files of 15621 points of full-length MuLV genomes. Dot matrix was constructed using DOTPLOT programs of the Wisconsin Package, Version 9.0, Genetics Computer Group (GCG), Madison WI and Vector <t>NTI</t> (Invitrogen, <t>Carlsbad,</t> California) tool with windows setting at 21 and stringency at 44. This analysis compares each nucleotide position with the corresponding position of another genome (Dot). Solid diagonal line represents similarity and broken lines indicate gaps. Although Dot-Matrix analyses were performed on several MuLV strains, viruses that showed high similarity scores are shown in panels A, B and C (see Additional File 2). Dot Matrix analyses of full-length genomic sequences shown include ; Panel A, Cas-Br-E [25] (X57540); Panel B, AKV (J01998), and Panel C, Moloney (J02255). The highest nucleotide similarity is observed with the CAS-Br-E ecotropic virus isolated from a Southern California Wild mouse with paralysis (Panel A). This is followed by Moloney [8] and AKV MuLV strains [85] (Panels B C respectively) . Note, the env sequences of MuLV-1313 are totally unrelated to all three viruses shown by large gap in this area of the diagonal line. In addition, note the numerous broken lines in gag and pol regions of the Moloney and AKV MuLV genomes.
    Vector Nti Advance, supplied by Thermo Fisher, used in various techniques. Bioz Stars score: 94/100, based on 376 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Thermo Fisher vector nti advance 11 software
    Dot Martrix analyses of the whole MuLV-1313 genome . Dot plots of the MuLV-1313 genome (GenBank accession number AF411814 ) were constructed utilizing the COMPARE which produced files of 15621 points of full-length MuLV genomes. Dot matrix was constructed using DOTPLOT programs of the Wisconsin Package, Version 9.0, Genetics Computer Group (GCG), Madison WI and Vector <t>NTI</t> (Invitrogen, <t>Carlsbad,</t> California) tool with windows setting at 21 and stringency at 44. This analysis compares each nucleotide position with the corresponding position of another genome (Dot). Solid diagonal line represents similarity and broken lines indicate gaps. Although Dot-Matrix analyses were performed on several MuLV strains, viruses that showed high similarity scores are shown in panels A, B and C (see Additional File 2). Dot Matrix analyses of full-length genomic sequences shown include ; Panel A, Cas-Br-E [25] (X57540); Panel B, AKV (J01998), and Panel C, Moloney (J02255). The highest nucleotide similarity is observed with the CAS-Br-E ecotropic virus isolated from a Southern California Wild mouse with paralysis (Panel A). This is followed by Moloney [8] and AKV MuLV strains [85] (Panels B C respectively) . Note, the env sequences of MuLV-1313 are totally unrelated to all three viruses shown by large gap in this area of the diagonal line. In addition, note the numerous broken lines in gag and pol regions of the Moloney and AKV MuLV genomes.
    Vector Nti Advance 11 Software, supplied by Thermo Fisher, used in various techniques. Bioz Stars score: 89/100, based on 309 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    91
    Thermo Fisher vector nti advance 11
    Genomic illustration of all four  NcHMA4  tandem repeats. Exons are represented by orange squares flanked by introns (blue lines). The  NcHMA4  library probe (yellow box) is illustrated at its site of hybridisation for each copy. Numbers above exons and below introns represent percentage sequence identities for each copy to a consensus  NcHMA4  sequence using Dot Matrix (Vector NTI 11).
    Vector Nti Advance 11, supplied by Thermo Fisher, used in various techniques. Bioz Stars score: 91/100, based on 342 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    InforMax Inc vector nti software
    Genomic illustration of all four  NcHMA4  tandem repeats. Exons are represented by orange squares flanked by introns (blue lines). The  NcHMA4  library probe (yellow box) is illustrated at its site of hybridisation for each copy. Numbers above exons and below introns represent percentage sequence identities for each copy to a consensus  NcHMA4  sequence using Dot Matrix (Vector NTI 11).
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    InforMax Inc vector nti
    The genetic organization of Saccharomyces <t>mtDNA.</t> For simpler comparison, the circular genomes, exported from Vector <t>NTI,</t> were aligned at the beginning of the large rRNA subunit ( rnl ). Protein-coding genes, ribosomal RNA, rnpB are marked as arrows and bar, tRNA genes as black lines, introns with white rectangles, intronic and free-standing ORFs by gray arrows and replication origins with black circles. Gene nomenclature follows the rules described in GOBASE ( atp for ATP synthetase subunits, cox for cytochrome oxidase subunits, cob for cytochrome b, rns for small rRNA ribosomal subunit, rnl for large rRNA ribosomal subunit, T2, C, H, etc. for particular tRNA coding genes, rps3 for ribosomal protein and rnpB for the RNA subunit of RNase P). Sizes are given on the bottom line in kbp.
    Vector Nti, supplied by InforMax Inc, used in various techniques. Bioz Stars score: 92/100, based on 102 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Thermo Fisher vector nti advance 11 5
    The genetic organization of Saccharomyces <t>mtDNA.</t> For simpler comparison, the circular genomes, exported from Vector <t>NTI,</t> were aligned at the beginning of the large rRNA subunit ( rnl ). Protein-coding genes, ribosomal RNA, rnpB are marked as arrows and bar, tRNA genes as black lines, introns with white rectangles, intronic and free-standing ORFs by gray arrows and replication origins with black circles. Gene nomenclature follows the rules described in GOBASE ( atp for ATP synthetase subunits, cox for cytochrome oxidase subunits, cob for cytochrome b, rns for small rRNA ribosomal subunit, rnl for large rRNA ribosomal subunit, T2, C, H, etc. for particular tRNA coding genes, rps3 for ribosomal protein and rnpB for the RNA subunit of RNase P). Sizes are given on the bottom line in kbp.
    Vector Nti Advance 11 5, supplied by Thermo Fisher, used in various techniques. Bioz Stars score: 99/100, based on 261 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Thermo Fisher vector nti 10 3 0
    The genetic organization of Saccharomyces <t>mtDNA.</t> For simpler comparison, the circular genomes, exported from Vector <t>NTI,</t> were aligned at the beginning of the large rRNA subunit ( rnl ). Protein-coding genes, ribosomal RNA, rnpB are marked as arrows and bar, tRNA genes as black lines, introns with white rectangles, intronic and free-standing ORFs by gray arrows and replication origins with black circles. Gene nomenclature follows the rules described in GOBASE ( atp for ATP synthetase subunits, cox for cytochrome oxidase subunits, cob for cytochrome b, rns for small rRNA ribosomal subunit, rnl for large rRNA ribosomal subunit, T2, C, H, etc. for particular tRNA coding genes, rps3 for ribosomal protein and rnpB for the RNA subunit of RNase P). Sizes are given on the bottom line in kbp.
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    Thermo Fisher vector nti advance sequence analysis software dynamic license
    The genetic organization of Saccharomyces <t>mtDNA.</t> For simpler comparison, the circular genomes, exported from Vector <t>NTI,</t> were aligned at the beginning of the large rRNA subunit ( rnl ). Protein-coding genes, ribosomal RNA, rnpB are marked as arrows and bar, tRNA genes as black lines, introns with white rectangles, intronic and free-standing ORFs by gray arrows and replication origins with black circles. Gene nomenclature follows the rules described in GOBASE ( atp for ATP synthetase subunits, cox for cytochrome oxidase subunits, cob for cytochrome b, rns for small rRNA ribosomal subunit, rnl for large rRNA ribosomal subunit, T2, C, H, etc. for particular tRNA coding genes, rps3 for ribosomal protein and rnpB for the RNA subunit of RNase P). Sizes are given on the bottom line in kbp.
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    InforMax Inc vector nti suite
    The genetic organization of Saccharomyces <t>mtDNA.</t> For simpler comparison, the circular genomes, exported from Vector <t>NTI,</t> were aligned at the beginning of the large rRNA subunit ( rnl ). Protein-coding genes, ribosomal RNA, rnpB are marked as arrows and bar, tRNA genes as black lines, introns with white rectangles, intronic and free-standing ORFs by gray arrows and replication origins with black circles. Gene nomenclature follows the rules described in GOBASE ( atp for ATP synthetase subunits, cox for cytochrome oxidase subunits, cob for cytochrome b, rns for small rRNA ribosomal subunit, rnl for large rRNA ribosomal subunit, T2, C, H, etc. for particular tRNA coding genes, rps3 for ribosomal protein and rnpB for the RNA subunit of RNase P). Sizes are given on the bottom line in kbp.
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    Image Search Results


    Dot Martrix analyses of the whole MuLV-1313 genome . Dot plots of the MuLV-1313 genome (GenBank accession number AF411814 ) were constructed utilizing the COMPARE which produced files of 15621 points of full-length MuLV genomes. Dot matrix was constructed using DOTPLOT programs of the Wisconsin Package, Version 9.0, Genetics Computer Group (GCG), Madison WI and Vector NTI (Invitrogen, Carlsbad, California) tool with windows setting at 21 and stringency at 44. This analysis compares each nucleotide position with the corresponding position of another genome (Dot). Solid diagonal line represents similarity and broken lines indicate gaps. Although Dot-Matrix analyses were performed on several MuLV strains, viruses that showed high similarity scores are shown in panels A, B and C (see Additional File 2). Dot Matrix analyses of full-length genomic sequences shown include ; Panel A, Cas-Br-E [25] (X57540); Panel B, AKV (J01998), and Panel C, Moloney (J02255). The highest nucleotide similarity is observed with the CAS-Br-E ecotropic virus isolated from a Southern California Wild mouse with paralysis (Panel A). This is followed by Moloney [8] and AKV MuLV strains [85] (Panels B C respectively) . Note, the env sequences of MuLV-1313 are totally unrelated to all three viruses shown by large gap in this area of the diagonal line. In addition, note the numerous broken lines in gag and pol regions of the Moloney and AKV MuLV genomes.

    Journal: Virology Journal

    Article Title: Molecular and phylogenetic analyses of a new Amphotropic murine leukemia virus (MuLV-1313)

    doi: 10.1186/1743-422X-3-101

    Figure Lengend Snippet: Dot Martrix analyses of the whole MuLV-1313 genome . Dot plots of the MuLV-1313 genome (GenBank accession number AF411814 ) were constructed utilizing the COMPARE which produced files of 15621 points of full-length MuLV genomes. Dot matrix was constructed using DOTPLOT programs of the Wisconsin Package, Version 9.0, Genetics Computer Group (GCG), Madison WI and Vector NTI (Invitrogen, Carlsbad, California) tool with windows setting at 21 and stringency at 44. This analysis compares each nucleotide position with the corresponding position of another genome (Dot). Solid diagonal line represents similarity and broken lines indicate gaps. Although Dot-Matrix analyses were performed on several MuLV strains, viruses that showed high similarity scores are shown in panels A, B and C (see Additional File 2). Dot Matrix analyses of full-length genomic sequences shown include ; Panel A, Cas-Br-E [25] (X57540); Panel B, AKV (J01998), and Panel C, Moloney (J02255). The highest nucleotide similarity is observed with the CAS-Br-E ecotropic virus isolated from a Southern California Wild mouse with paralysis (Panel A). This is followed by Moloney [8] and AKV MuLV strains [85] (Panels B C respectively) . Note, the env sequences of MuLV-1313 are totally unrelated to all three viruses shown by large gap in this area of the diagonal line. In addition, note the numerous broken lines in gag and pol regions of the Moloney and AKV MuLV genomes.

    Article Snippet: Dot matrix was constructed using DOTPLOT programs of the Wisconsin Package, Version 9.0, Genetics Computer Group (GCG), Madison WI and Vector NTI (Invitrogen, Carlsbad, California) tool with windows setting at 21 and stringency at 44.

    Techniques: Construct, Produced, Plasmid Preparation, Genomic Sequencing, Isolation

    Phylogenetic analyses of full Length MuLV genomes . Full-length nucleotide sequences as well as deduced amino acid sequences of 15 MuLV strains including MuLV-1313 were aligned and all gaps were stripped from the alignments before the phylogenetic trees were constructed and bootstrapping was set at 1000. Phylogenetic analyses were performed using PHYLIP [66, 71]. PHYLIP packages SEQBOOT, PROTDIST, DNADIST, NEIGHBOR, CONSENSE, and DRAWGRAM. The original data set was first analyzed by SEQBOOT which produced 100 bootstrapped data sets. The distance matrices on these data sets were achieved using PROTDIST for amino acid sequences and DNADIST for nucleotide sequences. The distance matrices were joined using NEIGHBOR. The tree files from NEIGHBOR were then applied with CONSENSE and the consensus tree was drawn using DRAWGRAM. Multiple sequence alignment were made using Vector NTI (Invitrogen, Carlsbad, California) with default gap opening penalty of 15 and default gap extension penalty of 6.66. Full length genomes used in the construction of the dendrogram included; AKV MuLV (J01998), MuLV 1313 (AF411814), Cas-Br-E MuLV (X57540), Friend-57 MuLV (X02794), Friend FB29 MuLV (Z11128), Friend PVC211 MuLV (M93134), Friend (FrC6-A8F5 D88386), mink cell focus-forming virus 1233 (MCF1233, U13766), Moloney MuLV (J02255), radiation leukemia virus (RadLV, K03363), Rauscher MuLV (Rauscher, U94692), SL3-3 MuLV (AF169256), solid-type reticulum cell sarcoma 19-6 MuLV (SRS 19-6, AF019230), HEMV (AY818896) and MDEV (AF053745). Note that both the amphotropic MuLV-1313 and ecotropic Cas-Br-E MuLV of the Southern California feral mice arise from a separate node of the phylogenetic tree indicating their evolutionary relationship.

    Journal: Virology Journal

    Article Title: Molecular and phylogenetic analyses of a new Amphotropic murine leukemia virus (MuLV-1313)

    doi: 10.1186/1743-422X-3-101

    Figure Lengend Snippet: Phylogenetic analyses of full Length MuLV genomes . Full-length nucleotide sequences as well as deduced amino acid sequences of 15 MuLV strains including MuLV-1313 were aligned and all gaps were stripped from the alignments before the phylogenetic trees were constructed and bootstrapping was set at 1000. Phylogenetic analyses were performed using PHYLIP [66, 71]. PHYLIP packages SEQBOOT, PROTDIST, DNADIST, NEIGHBOR, CONSENSE, and DRAWGRAM. The original data set was first analyzed by SEQBOOT which produced 100 bootstrapped data sets. The distance matrices on these data sets were achieved using PROTDIST for amino acid sequences and DNADIST for nucleotide sequences. The distance matrices were joined using NEIGHBOR. The tree files from NEIGHBOR were then applied with CONSENSE and the consensus tree was drawn using DRAWGRAM. Multiple sequence alignment were made using Vector NTI (Invitrogen, Carlsbad, California) with default gap opening penalty of 15 and default gap extension penalty of 6.66. Full length genomes used in the construction of the dendrogram included; AKV MuLV (J01998), MuLV 1313 (AF411814), Cas-Br-E MuLV (X57540), Friend-57 MuLV (X02794), Friend FB29 MuLV (Z11128), Friend PVC211 MuLV (M93134), Friend (FrC6-A8F5 D88386), mink cell focus-forming virus 1233 (MCF1233, U13766), Moloney MuLV (J02255), radiation leukemia virus (RadLV, K03363), Rauscher MuLV (Rauscher, U94692), SL3-3 MuLV (AF169256), solid-type reticulum cell sarcoma 19-6 MuLV (SRS 19-6, AF019230), HEMV (AY818896) and MDEV (AF053745). Note that both the amphotropic MuLV-1313 and ecotropic Cas-Br-E MuLV of the Southern California feral mice arise from a separate node of the phylogenetic tree indicating their evolutionary relationship.

    Article Snippet: Dot matrix was constructed using DOTPLOT programs of the Wisconsin Package, Version 9.0, Genetics Computer Group (GCG), Madison WI and Vector NTI (Invitrogen, Carlsbad, California) tool with windows setting at 21 and stringency at 44.

    Techniques: Construct, Produced, Sequencing, Plasmid Preparation, Mouse Assay

    In silico analysis of Hmgpi expression. ( A ) Previous microarray analysis of Hmgpi expression. Hmgpi expression appeared at the 2-cell stage, peaked at the 4-cell stage and then decreased ( 3 ). ( B ) Expression sequence tag (EST) frequencies in Unigene cDNA libraries. Out of 4.7 million mouse ESTs, 16 Hmgpi clones were exclusively detected at the cleavage stages: 9, 2 and 5 ESTs from 2-cell, 4-cell and 8-cell libraries, respectively. ( C ) Exon–intron structures and a putative protein structure of Hmgpi. Hmgpi has three exon–intron models and one protein model. Predicted protein domains are also shown. ( D ) Conserved domains of Hmgpi / Ubtfl1 gene in mouse, rat and human. Pairwise alignment scores of conserved domains between species were shown. ( E ) Phylogenetic tree of gene nucleotide acid sequences containing HMG domains determined by a sequence distance method and the neighbour-joining (NJ) algorithm ( 41 ) using Vector NTI software (Invitrogen, Carlsbad, CA, USA).

    Journal: Human Molecular Genetics

    Article Title: Involvement of a novel preimplantation-specific gene encoding the high mobility group box protein Hmgpi in early embryonic development

    doi: 10.1093/hmg/ddp512

    Figure Lengend Snippet: In silico analysis of Hmgpi expression. ( A ) Previous microarray analysis of Hmgpi expression. Hmgpi expression appeared at the 2-cell stage, peaked at the 4-cell stage and then decreased ( 3 ). ( B ) Expression sequence tag (EST) frequencies in Unigene cDNA libraries. Out of 4.7 million mouse ESTs, 16 Hmgpi clones were exclusively detected at the cleavage stages: 9, 2 and 5 ESTs from 2-cell, 4-cell and 8-cell libraries, respectively. ( C ) Exon–intron structures and a putative protein structure of Hmgpi. Hmgpi has three exon–intron models and one protein model. Predicted protein domains are also shown. ( D ) Conserved domains of Hmgpi / Ubtfl1 gene in mouse, rat and human. Pairwise alignment scores of conserved domains between species were shown. ( E ) Phylogenetic tree of gene nucleotide acid sequences containing HMG domains determined by a sequence distance method and the neighbour-joining (NJ) algorithm ( 41 ) using Vector NTI software (Invitrogen, Carlsbad, CA, USA).

    Article Snippet: Orthologous relationships between HMG family genes were identified from phylogenetic-tree amino acid sequences determined by a sequence distance method and the Neighbor Joining (NJ) algorithm ( ) using Vector NTI software (Invitrogen, Carlsbad, CA, USA).

    Techniques: In Silico, Expressing, Microarray, Sequencing, Clone Assay, Plasmid Preparation, Software

    Genomic illustration of all four  NcHMA4  tandem repeats. Exons are represented by orange squares flanked by introns (blue lines). The  NcHMA4  library probe (yellow box) is illustrated at its site of hybridisation for each copy. Numbers above exons and below introns represent percentage sequence identities for each copy to a consensus  NcHMA4  sequence using Dot Matrix (Vector NTI 11).

    Journal: PLoS ONE

    Article Title: Tandem Quadruplication of HMA4 in the Zinc (Zn) and Cadmium (Cd) Hyperaccumulator Noccaea caerulescens

    doi: 10.1371/journal.pone.0017814

    Figure Lengend Snippet: Genomic illustration of all four NcHMA4 tandem repeats. Exons are represented by orange squares flanked by introns (blue lines). The NcHMA4 library probe (yellow box) is illustrated at its site of hybridisation for each copy. Numbers above exons and below introns represent percentage sequence identities for each copy to a consensus NcHMA4 sequence using Dot Matrix (Vector NTI 11).

    Article Snippet: Image created through Vector NTI 11 (Invitrogen, Paisley, UK). (TIF) Click here for additional data file.

    Techniques: Hybridization, Sequencing, Plasmid Preparation

    ). The backbone is rendered as ribbons. The α-subunit residues homologous to the human δ-subunit residues R366, V541, and P579 were determined by sequence alignment using Vector NTI 11.0 (Invitrogen, Carlsbad, CA). Side chains are shown in CPK mode, with carbon in yellow and nitrogen in blue. Individual domains within the extracellular region are labeled.

    Journal: American Journal of Respiratory Cell and Molecular Biology

    Article Title: The Epithelial Sodium Channel Is a Modifier of the Long-Term Nonprogressive Phenotype Associated with F508del CFTR Mutations

    doi: 10.1165/rcmb.2017-0166OC

    Figure Lengend Snippet: ). The backbone is rendered as ribbons. The α-subunit residues homologous to the human δ-subunit residues R366, V541, and P579 were determined by sequence alignment using Vector NTI 11.0 (Invitrogen, Carlsbad, CA). Side chains are shown in CPK mode, with carbon in yellow and nitrogen in blue. Individual domains within the extracellular region are labeled.

    Article Snippet: The α-subunit residues homologous to the human δ-subunit residues R366, V541, and P579 were determined by sequence alignment using Vector NTI 11.0 (Invitrogen). δR366 is located in the finger domain of the extracellular region of the channel ( ). δV541 and δP579 are located within loops at the base and top of the thumb domain, respectively. ) using PyMol 1.5 (

    Techniques: Sequencing, Plasmid Preparation, Labeling

    The genetic organization of Saccharomyces mtDNA. For simpler comparison, the circular genomes, exported from Vector NTI, were aligned at the beginning of the large rRNA subunit ( rnl ). Protein-coding genes, ribosomal RNA, rnpB are marked as arrows and bar, tRNA genes as black lines, introns with white rectangles, intronic and free-standing ORFs by gray arrows and replication origins with black circles. Gene nomenclature follows the rules described in GOBASE ( atp for ATP synthetase subunits, cox for cytochrome oxidase subunits, cob for cytochrome b, rns for small rRNA ribosomal subunit, rnl for large rRNA ribosomal subunit, T2, C, H, etc. for particular tRNA coding genes, rps3 for ribosomal protein and rnpB for the RNA subunit of RNase P). Sizes are given on the bottom line in kbp.

    Journal: DNA Research: An International Journal for Rapid Publication of Reports on Genes and Genomes

    Article Title: The evolutionary history of Saccharomyces species inferred from completed mitochondrial genomes and revision in the ‘yeast mitochondrial genetic code’

    doi: 10.1093/dnares/dsx026

    Figure Lengend Snippet: The genetic organization of Saccharomyces mtDNA. For simpler comparison, the circular genomes, exported from Vector NTI, were aligned at the beginning of the large rRNA subunit ( rnl ). Protein-coding genes, ribosomal RNA, rnpB are marked as arrows and bar, tRNA genes as black lines, introns with white rectangles, intronic and free-standing ORFs by gray arrows and replication origins with black circles. Gene nomenclature follows the rules described in GOBASE ( atp for ATP synthetase subunits, cox for cytochrome oxidase subunits, cob for cytochrome b, rns for small rRNA ribosomal subunit, rnl for large rRNA ribosomal subunit, T2, C, H, etc. for particular tRNA coding genes, rps3 for ribosomal protein and rnpB for the RNA subunit of RNase P). Sizes are given on the bottom line in kbp.

    Article Snippet: Individual contigs with mtDNA segments were assembled into a single molecule using the Vector NTI v.9.0 (v.10) software package from InforMax, Inc.

    Techniques: Plasmid Preparation