Vector nti advanced 11

Manufactured by Thermo Fisher Scientific

Sourced in United States

Vector NTI Advanced 11.5.4 is a software tool for molecular biology and bioinformatics analysis. It provides a suite of tools for DNA and protein sequence analysis, including sequence alignment, annotation, and visualization.

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Lab products found in correlation

Align x, by Thermo Fisher Scientific (3 mentions) Revertaid first strand cdna synthesis kit, by Thermo Fisher Scientific (2 mentions) Megabace 1000, by Cytiva (1 mentions) Ptc 225, by Bio-Rad (1 mentions) Exosap it, by GE Healthcare (1 mentions) Dna stool mini kit, by Qiagen (1 mentions) Qiaquick spin column, by Qiagen (1 mentions) Abi 3730 capillary electrophoresis genetic analyzer, by Thermo Fisher Scientific (1 mentions) Rnaiso plus trizol, by Takara Bio (1 mentions) Pmd19 t vector, by Takara Bio (1 mentions)

Spelling variants of this product

Vector NTI (116 citations) Vector NTI 11.5 software (40 citations)

7 protocols using vector nti advanced 11

Sequence Alignment of Aptamers

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Example 4

Alignment of SEQ ID NO 1 to SEQ ID NO 100 is performed using the software Align X, a component of Vector NTI Advanced 11.5.4 by Invitrogen. Several groups of sequences have at least 90%, at least 70%, or at least 50% nucleotide sequence identity as illustrated in the alignments of FIGS. 9, 10, and 11. In these alignments, only the central variable region of the aptamers is included for simplicity. Thus, oligonucleotides with at least 50%, at least 70%, or at least 90% nucleotide sequence identity to sequences selected from the group consisting of SEQ ID NO 1 to SEQ ID NO 100 are included and may be part of the current invention.

US11384357B2. Aptamers for personal care applications (2022-07-12). The Procter & Gamble Company [US]. Inventors: Juan Esteban Velasquez [US], Amy Violet Trejo [US], Laurie Ellen Breyfogle [US], James Patrick Henry [US], Douglas Joseph Dobrozsi [US], Gregory Allen Penner [CA].

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Nucleotide Sequence Alignment of Aptamers

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Example 16

Alignment of SEQ ID NO 1 to SEQ ID NO 400 was performed using the software Align X, a component of Vector NTI Advanced 11.5.4 by Invitrogen. Several groups of sequences have at least 90%, at least 70%, or at least 50% nucleotide sequence identity as illustrated in the alignments of FIGS. 5, 6, and 7. In these alignments, only the central variable region of the aptamers was included for simplicity. Thus, oligonucleotides with at least 50%, at least 70%, or at least 90% nucleotide sequence identity to sequences selected from the group consisting of SEQ ID NO 1 to SEQ ID NO 400 are included as part of the current invention. FIG. 5 shows the alignment of exemplary sequences with at least 90% nucleotide sequence identity that are identified during the selection process. FIG. 6 shows the alignment of exemplary sequences with at least 70% nucleotide sequence identity that are identified during the selection process. FIG. 7 shows the alignment of exemplary sequences with at least 50% nucleotide sequence identity that are identified during the selection process.

US11806419B2. Aptamers for odor control applications (2023-11-07). The Procter & Gamble Company [US]. Inventors: Juan Esteban Velasquez [US], Amy Violet Trejo [US], Gregory Allen Penner [CA], Stevan David Jones [US].

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Sequence Alignment and Identity Analysis

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Example 3

Alignment of SEQ ID NO: 1 to SEQ ID NO: 100 was performed using the software Align X, a component of Vector NTI Advanced 11.5.4 by Invitrogen. Several groups of sequences have at least 90%, at least 70%, or at least 50% nucleotide sequence identity as illustrated in the alignments of FIGS. 13, 14, and 15. In these alignments, only the central variable region of the aptamers was included for simplicity. Thus, oligonucleotides with at least 50%, at least 70%, or at least 90% nucleotide sequence identity to sequences selected from the group consisting of SEQ ID NO: 1 to SEQ ID NO: 200 are included as part of the current invention.

US11859187B2. Aptamers for personal health care applications (2024-01-02). The Procter & Gamble Company [US]. Inventors: Juan Esteban Velasquez [US], Spencer Christopher Rupard [US], Amy Violet Trejo [US], Adam Michael Pitz [US], Kelly Lee Schmeichel [US], Erin Nicole Swigart [US], Gregory Allen Penner [CA].

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Cryptosporidium Phylogenetic Analysis Protocol

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Sequences were analyzed and consensus sequences were generated using the Vector NTI Advanced 11 software (Invitrogen). Consensus sequences were compared to Cryptosporidium sequences in the GenBank using NCBI′s online BLAST tool with the default algorithm parameters to target 100 sequences (http://blast.ncbi.nlm.nih.gov/) (12 March, 2020, as last day accessed). A phylogenetic tree was constructed using the Vector NTI Advance 11 based on a pairwise alignment. Depending on the availability of the 18S rRNA gene sequences of Cryptosporidium in the GenBank, reference sequences for constructing the phylogenetic trees were selected based on: (1) sequences representing well described Cryptosporidium species from fish, amphibians, reptiles, birds, and mammals; (2) sequences of known zoonotic genotypes; (3) sequences previously used by other investigators for species description or as reference sequences; (4) sequence length (longer sequence available for each species; i.e., ≥700 bp); and (5) sequences not originating from cloned PCR products due to the potential for erroneous sequence data generated from cloning PCR products [27 (link),28 (link)]. Names and GenBank accession numbers of selected references sequences are shown in Figure 1.

Li X., Nguyen T., Xiao C., Levy A., Akagi Y., Silkie S, & Atwill E.R. (2020). Prevalence and Genotypes of Cryptosporidium in Wildlife Populations Co-Located in a Protected Watershed in the Pacific Northwest, 2013 to 2016. Microorganisms, 8(6), 914.

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ITS2 Amplification and Sequencing Protocol

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The internal transcribed spacer 2 (ITS2) part of the nuclear ribosomal DNA was amplified with the primer pair ITS2/ITS4 according to White, Bruns, Lee and Taylor (1990) on a PTC-225 (Peltier Thermal Cycler, MJ Research, Waltham, MA, USA). PCR amplicons were purified with ExoSap IT (GE healthcare, Buckinghamshire, UK) according to the manufacturer’s procedure and visualized on standard agarose gel to ensure the presence of single-band products. Both strands of the PCR amplicons were sequenced with the PCR primers using DYEnamic ET dye terminator chemistry (Amersham Biosciences, Chicago, IL, USA), purified on AutoSeq96 (Amersham Biosciences) plates, diluted with 10 µL of MQ-water and subsequently analyzed on a MegaBace 1000 (Amersham Biosciences). Sequences were analyzed in Vector NTI Advanced 11 (Invitrogen, Waltham, MA, USA) and assembled in BioEdit 7.0.9.0 [29 ].

Elameen A., Stueland S., Kristensen R., Fristad R.F., Vrålstad T, & Skaar I. (2021). Genetic Analyses of Saprolegnia Strains Isolated from Salmonid Fish of Different Geographic Origin Document the Connection between Pathogenicity and Molecular Diversity. Journal of Fungi, 7(9), 713.

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Cryptosporidium Genotyping from Fecal Samples

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All fecal samples that were microscopic positive of Cryptosporidium oocysts were subjected to genotyping of Cryptosporidium. A 0.2 g of fresh feces was exposed to 5 cycles of freeze (−80 °C) and thaw (+70 °C), and then used for DNA extraction by using the DNA Stool Mini Kit (Qiagen, Hilden, Germany) according to the manufacturer’s instructions. All DNA samples were stored at −20 °C until further analysis. A nested PCR was performed on DNA samples using primers and reaction conditions amplifying an ~830 bp fragment of the 18S rRNA gene according to methods previously described [49 (link),50 (link)]. A DNA template of C. parvum isolated from calves from a local dairy farm was used as a positive control, and a negative control without DNA template was included. PCR products were verified by electrophoresis in 2% agarose gel stained with ethidium bromide. Products of the secondary PCR were purified using Qiaquick spin columns (Qiagen) and sequenced at the UC Davis DNA Sequencing Facility using an ABI 3730 capillary electrophoresis genetic analyzer (Applied Biosystems Inc., Foster City, CA, USA). Primers of the secondary PCR were used for sequencing in both forward and reverse directions. Consensus sequences were generated from the forward and reverse sequences of each isolate using Vector NTI Advanced 11 software (Invitrogen Corporation, Carlsbad, CA, USA).

Li X., Vodovoza T, & Atwill E.R. (2022). Diverse Genotypes of Cryptosporidium in Sheep in California, USA. Pathogens, 11(9), 1023.

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Cloning Kelch Motif ACBPs from Brassica napus

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Kelch motif ACBPs were cloned from B. napus that were grown for 60 days in Huazhong University of Science and Technology, Wuhan, China (semi winter-type rapeseed growing area). The oil content of the material was about 50 %. We conducted RNA extraction from siliques, by using Trizol RNA isoplus (Takara). To synthesize the first cDNA strand, RevertAid First Strand cDNA Synthesis Kit by Thermo Scientific was used. Primers were designed based on kelch motif BrACBPs and BoACBPs sequences. Oligo7 software was operated to design these primers (sequences in Table S1, Additional file 7). The amplification was performed with KOD enzyme and then with ES Taq enzyme. The targeted genes were purified by CWBIO Gel extraction kit. They were then inserted into T-vector PMD19 by Takara Bio Inc. and integrated into E. coli DH5- α. Genes from positive colonies were consequently sequenced. Vector NTI Advanced 11 software (Invitrogen Corporation) was used to align the obtained sequences with CDS of BrACBPs and BoACBPs to acquire CDS of BnACBPs, which were translated into protein sequences. Additionally, all four classes of BnACBPs were acquired from the CNS-Genoscope database (http://www.genoscope.cns.fr/brassicanapus/) [24 ] with BrACBPs and BoACBPs as query.

Raboanatahiry N.H., Yin Y., Chen L, & Li M. (2015). Genome-wide identification and Phylogenic analysis of kelch motif containing ACBP in Brassica napus. BMC Genomics, 16(1), 512.

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