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Journal articles on the topic 'Sequencer'

Author: Grafiati

Published: 4 June 2021

Last updated: 9 February 2022

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1

McKay, D. J., B. S. Renaux, and G. H. Dixon. "The amino acid sequence of human sperm protamine P1." Bioscience Reports 5, no. 5 (May 1, 1985): 383–91. http://dx.doi.org/10.1007/bf01116555.

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Human sperm protamines have been extracted from spermatozoa pooled from several donors, converted to their S-pyridylethylated derivatives and resolved into two major components, P1 and PI, by Bio-Rex 70 chromatography. Protamine P1 was further purified by Bio-Gel P-10 chromatography and sequenced directly on a gas phase protein sequencer for 43 residues. To complete the sequence, P1 was cleaved at methionine 36 and the C-terminal tetradecapeptide was purified by h.p.i.c, and sequenced completely. The 50 residue sequence is: 10 20 30 40 ARYRC CRSQS RSRYY RQRQR SRRRR RRSCQ TRRRA MRCCR 50 PRYRP R

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2

Xu, Liu, and Masahide Seki. "Recent advances in the detection of base modifications using the Nanopore sequencer." Journal of Human Genetics 65, no. 1 (October 11, 2019): 25–33. http://dx.doi.org/10.1038/s10038-019-0679-0.

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Abstract DNA and RNA modifications have important functions, including the regulation of gene expression. Existing methods based on short-read sequencing for the detection of modifications show difficulty in determining the modification patterns of single chromosomes or an entire transcript sequence. Furthermore, the kinds of modifications for which detection methods are available are very limited. The Nanopore sequencer is a single-molecule, long-read sequencer that can directly sequence RNA as well as DNA. Moreover, the Nanopore sequencer detects modifications on long DNA and RNA molecules.

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3

URANO, Gen, and Masanori KUNITA. "DNA Sequencer." Japanese Journal of Thrombosis and Hemostasis 1, no. 4 (1990): 357–61. http://dx.doi.org/10.2491/jjsth.1.357.

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4

Gabriel, Christian, Martin Danzer, Christa Hackl, Guido Kopal, Katja Hofer, Stephanie Stabentheiner, and Johannes Pröll. "215-P: Genome sequencer sequence-based HLA typing." Human Immunology 70 (November 2009): S120. http://dx.doi.org/10.1016/j.humimm.2009.09.248.

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5

Walker, J. E., I. M. Fearnley, and R. A. Blows. "A rapid solid-phase protein microsequencer." Biochemical Journal 237, no. 1 (July 1, 1986): 73–84. http://dx.doi.org/10.1042/bj2370073.

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A solid-phase protein microsequencer is described that has been designed to determine protein sequences with subnanomolar quantities of protein. Its utility has been demonstrated by the determination of many sequences in subunits of mitochondrial F1-ATPase, in a protein isolated from mouse gap junctions and in the mitochondrial phosphate-transporter protein. It has a number of advantages over liquid- and gas-phase sequencers. Firstly, the degradation cycle takes 24 min, more than twice as fast as any other sequencer. This helps to reduce exposure of proteins to inimical reagents and increases

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6

HIRANO, Hisashi. "Amino Acid Sequence Analysis by Gas-Phase Protein Sequencer." Journal of Japan Oil Chemists' Society 38, no. 10 (1989): 791–99. http://dx.doi.org/10.5650/jos1956.38.791.

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7

Bell, Steven. "The ‘logic’ sequencer." Electronics Education 1990, no. 2 (1990): 16–17. http://dx.doi.org/10.1049/ee.1990.0024.

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8

Md Isa, Mohd Nazrin, Sohiful Anuar Zainol Murad, Mohamad Imran Ahmad, Muhammad M. Ramli, and Rizalafande Che Ismail. "An Efficient Scheduling Technique for Biological Sequence Alignment." Applied Mechanics and Materials 754-755 (April 2015): 1087–92. http://dx.doi.org/10.4028/www.scientific.net/amm.754-755.1087.

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Computing alignment matrix score to search for regions of homology between biological sequences is time consuming task. This is due to the recursive nature of the dynamic programming-based algorithms such as the Smith-Waterman and the Needleman-Wunsch algorithmns. Typical FPGA-based protein sequencer comprises of two main logic blocks. One for computing alignment scores i.e. the processing element (PE), while another logic block for configuring the PE with coefficients. During alignment matrix computation, the logic block for configuring the PE are left unused until the time consuming alignmen

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9

Poole, Anthony M., Daniel B. Stouffer, and Jason M. Tylianakis. "‘Ecosystomics’: ecology by sequencer." Trends in Ecology & Evolution 27, no. 6 (June 2012): 309–10. http://dx.doi.org/10.1016/j.tree.2012.03.008.

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10

Dovichi, N. "Development of DNA Sequencer." Science 285, no. 5430 (August 13, 1999): 1013h—1013. http://dx.doi.org/10.1126/science.285.5430.1013h.

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11

Ikeda, H. "Single shot FASTBUS sequencer." IEEE Transactions on Nuclear Science 36, no. 5 (1989): 1647–49. http://dx.doi.org/10.1109/23.41119.

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12

Park, Kyungmin, Seung-Ho Lee, Jongwoo Kim, Jingyeong Lee, Geum-Young Lee, Seungchan Cho, Seung Ho Lee, et al. "Multiplex PCR-Based Nanopore Sequencing and Epidemiological Surveillance of Hantaan orthohantavirus in Apodemus agrarius, Republic of Korea." Viruses 13, no. 5 (May 6, 2021): 847. http://dx.doi.org/10.3390/v13050847.

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Whole-genome sequencing of infectious agents enables the identification and characterization of emerging viruses. The MinION device is a portable sequencer that allows real-time sequencing in fields or hospitals. Hantaan orthohantavirus (Hantaan virus, HTNV), harbored by Apodemus agrarius, causes hemorrhagic fever with renal syndrome (HFRS) and poses a critical public health threat worldwide. In this study, we aimed to evaluate the feasibility of using nanopore sequencing for whole-genome sequencing of HTNV from samples having different viral copy numbers. Amplicon-based next-generation sequen

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13

Own, C., A. Bleloch, W. Lerach, C. Bowell, M. Hamalainen, J. Herschleb, C. Melville, J. Stark, M. Andregg, and W. Andregg. "First Nucleotide Sequence Data from an Electron Microscopy Based DNA Sequencer." Microscopy and Microanalysis 19, S2 (August 2013): 208–9. http://dx.doi.org/10.1017/s1431927613003036.

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14

Bhown, Ajit S., James L. Wayland, J. Daniel Lynn, and J. Claude Bennett. "Conversion of the Beckman liquid phase sequencer to a gas-liquid phase sequencer." Analytical Biochemistry 175, no. 1 (November 1988): 39–51. http://dx.doi.org/10.1016/0003-2697(88)90358-2.

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15

Kahrs, Mark, and Tom Killian. "Yamaha QY10 Synthesizer and Sequencer." Computer Music Journal 17, no. 1 (1993): 82. http://dx.doi.org/10.2307/3680580.

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16

Cikotte Leonard, J., Wayne Dannels, and R. McBride Thomas. "5349296 Magnetic resonance scan sequencer." Magnetic Resonance Imaging 13, no. 5 (January 1995): XIX. http://dx.doi.org/10.1016/0730-725x(95)98053-s.

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17

Hirabayashi, Aki, Koji Yahara, Satomi Mitsuhashi, So Nakagawa, Tadashi Imanishi, Van Thi Thu Ha, An Van Nguyen, Son Thai Nguyen, Keigo Shibayama та Masato Suzuki. "Plasmid analysis of NDM metallo-β-lactamase-producing Enterobacterales isolated in Vietnam". PLOS ONE 16, № 7 (28 липня 2021): e0231119. http://dx.doi.org/10.1371/journal.pone.0231119.

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Carbapenem-resistant Enterobacterales (CRE) represent a serious threat to public health due to the lack of treatment and high mortality. The rate of antimicrobial resistance of Enterobacterales isolates to major antimicrobials, including carbapenems, is much higher in Vietnam than in Western countries, but the reasons remain unknown due to the lack of genomic epidemiology research. A previous study suggested that carbapenem resistance genes, such as the carbapenemase gene blaNDM, spread via plasmids among Enterobacterales in Vietnam. In this study, we characterized blaNDM-carrying plasmids in

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18

Leigh, Deborah M., Christopher Schefer, and Carolina Cornejo. "Determining the Suitability of MinION’s Direct RNA and DNA Amplicon Sequencing for Viral Subtype Identification." Viruses 12, no. 8 (July 25, 2020): 801. http://dx.doi.org/10.3390/v12080801.

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The MinION sequencer is increasingly being used for the detection and outbreak surveillance of pathogens due to its rapid throughput. For RNA viruses, MinION’s new direct RNA sequencing is the next significant development. Direct RNA sequencing studies are currently limited and comparisons of its diagnostic performance relative to different DNA sequencing approaches are lacking as a result. We sought to address this gap and sequenced six subtypes from the mycovirus CHV-1 using MinION’s direct RNA sequencing and DNA sequencing based on a targeted viral amplicon. Reads from both techniques could

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19

Ozols, J., and J. M. Caron. "Posttranslational modification of tubulin by palmitoylation: II. Identification of sites of palmitoylation." Molecular Biology of the Cell 8, no. 4 (April 1997): 637–45. http://dx.doi.org/10.1091/mbc.8.4.637.

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As shown in the companion article, tubulin is posttranslationally modified in vivo by palmitoylation. Our goal in this study was to identify the palmitoylation sites by protein structure analysis. To obtain quantities of palmitoylated tubulin required for this analysis, a cell-free system for enzymatic [3H]palmitoylation was developed and characterized in our companion article. We then developed a methodology to examine directly the palmitoylation of all 451 amino acids of alpha-tubulin. 3H-labeled palmitoylated alpha-tubulin was cleaved with cyanogen bromide (CNBr). The CNBr digest was resolv

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20

S, Kana Saputra, Wisnu Ananta Kusuma, and Agus Buono. "Fuzzy-based Spectral Alignment for Correcting DNA Sequence from Next Generation Sequencer." TELKOMNIKA (Telecommunication Computing Electronics and Control) 14, no. 2 (June 1, 2016): 707. http://dx.doi.org/10.12928/telkomnika.v14i2.2395.

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21

Hagemann, Tracy L., and Sau-Ping Kwan. "ABI Sequencing Analysis: Manipulation of Sequence Data from the ABI DNA Sequencer." Molecular Biotechnology 13, no. 2 (1999): 137–52. http://dx.doi.org/10.1385/mb:13:2:137.

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22

Harrington, Colleen T., Elaine I. Lin, Matthew T. Olson, and James R. Eshleman. "Fundamentals of Pyrosequencing." Archives of Pathology & Laboratory Medicine 137, no. 9 (September 1, 2013): 1296–303. http://dx.doi.org/10.5858/arpa.2012-0463-ra.

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Context.—DNA sequencing is critical to identifying many human genetic disorders caused by DNA mutations, including cancer. Pyrosequencing is less complex, involves fewer steps, and has a superior limit of detection compared with Sanger sequencing. The fundamental basis of pyrosequencing is that pyrophosphate is released when a deoxyribonucleotide triphosphate is added to the end of a nascent strand of DNA. Because deoxyribonucleotide triphosphates are sequentially added to the reaction and because the pyrophosphate concentration is continuously monitored, the DNA sequence can be determined. Ob

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23

Drijver, Evert, Joep Stohr, Jaco Verweij, Carlo Verhulst, Francisca Velkers, Arjan Stegeman, Marjolein Bergh, Jan Kluytmans, and i.-Health Group. "Limited Genetic Diversity of blaCMY-2-Containing IncI1-pST12 Plasmids from Enterobacteriaceae of Human and Broiler Chicken Origin in The Netherlands." Microorganisms 8, no. 11 (November 8, 2020): 1755. http://dx.doi.org/10.3390/microorganisms8111755.

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Distinguishing epidemiologically related and unrelated plasmids is essential to confirm plasmid transmission. We compared IncI1–pST12 plasmids from both human and livestock origin and explored the degree of sequence similarity between plasmids from Enterobacteriaceae with different epidemiological links. Short-read sequence data of Enterobacteriaceae cultured from humans and broilers were screened for the presence of both a blaCMY-2 gene and an IncI1–pST12 replicon. Isolates were long-read sequenced on a MinION sequencer (OxfordNanopore Technologies). After plasmid reconstruction using hybrid

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24

Mafune, Korena K., Bruce J. Godfrey, Daniel J. Vogt, and Kristiina A. Vogt. "A rapid approach to profiling diverse fungal communities using the MinION™ nanopore sequencer." BioTechniques 68, no. 2 (February 2020): 72–78. http://dx.doi.org/10.2144/btn-2019-0072.

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The Oxford Nanopore Technologies MinION™ sequencer holds the capability to generate long amplicon reads; however, only a small amount of information is available regarding methodological approaches and the ability to identify a broad diversity of fungal taxa. To assess capabilities, three fungal mock communities were sequenced, each of which had varying ratios of 16 taxa. The data were processed through our selected pipeline. The MinION recovered all mock community members, when mixed at equal ratios. When a taxon was represented at a lower ratio, it was not recovered or decreased in relative

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25

Tanaka, Mami, Sayaka Mino, Yoshitoshi Ogura, Tetsuya Hayashi, and Tomoo Sawabe. "Availability of Nanopore sequences in the genome taxonomy for Vibrionaceae systematics: Rumoiensis clade species as a test case." PeerJ 6 (June 18, 2018): e5018. http://dx.doi.org/10.7717/peerj.5018.

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Whole genome sequence comparisons have become essential for establishing a robust scheme in bacterial taxonomy. To generalize this genome-based taxonomy, fast, reliable, and cost-effective genome sequencing methodologies are required. MinION, the palm-sized sequencer from Oxford Nanopore Technologies, enables rapid sequencing of bacterial genomes using minimal laboratory resources. Here we tested the ability of Nanopore sequences for the genome-based taxonomy of Vibrionaceae and compared Nanopore-only assemblies to complete genomes of five Rumoiensis clade species: Vibrio aphrogenes, V. algivo

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26

Loman, Nick, Sarah Goodwin, Hans J. Jansen, and Matt Loose. "A disruptive sequencer meets disruptive publishing." F1000Research 4 (October 15, 2015): 1074. http://dx.doi.org/10.12688/f1000research.7229.1.

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Nanopore sequencing was recently made available to users in the form of the Oxford Nanopore MinION. Released to users through an early access programme, the MinION is made unique by its tiny form factor and ability to generate very long sequences from single DNA molecules. The platform is undergoing rapid evolution with three distinct nanopore types and five updates to library preparation chemistry in the last 18 months. To keep pace with the rapid evolution of this sequencing platform, and to provide a space where new analysis methods can be openly discussed, we present a new F1000Research ch

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27

Barber, Karl W., and Stephen J. Elledge. "Sequencer Hacking Unlocks Quantitative Protein Studies." Molecular Cell 73, no. 5 (March 2019): 863–65. http://dx.doi.org/10.1016/j.molcel.2019.01.039.

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28

Rothstein, Joseph. "Twelve Tone Systems Cakewalk Sequencer Software." Computer Music Journal 13, no. 2 (1989): 96. http://dx.doi.org/10.2307/3680048.

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29

LEWIN, R. "Japanese Super-Sequencer Poised to Roll." Science 236, no. 4797 (April 3, 1987): 31. http://dx.doi.org/10.1126/science.236.4797.31.

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30

Marx, Vivien. "Nanopores: a sequencer in your backpack." Nature Methods 12, no. 11 (October 29, 2015): 1015–18. http://dx.doi.org/10.1038/nmeth.3625.

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31

Kulkarni, C. M. "Design Optimisation of Parachute Sequencer Mechanism." Defence Science Journal 42, no. 1 (January 1, 1992): 23–28. http://dx.doi.org/10.14429/dsj.42.4345.

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32

O’Brien, Kevin M., Jonathan Wren, Varshal K. Davé, Diane Bai, Richard D. Anderson, Simon Rayner, Glen A. Evans, Ali E. Dabiri, and Harold R. Garner. "ASTRAL, a hyperspectral imaging DNA sequencer." Review of Scientific Instruments 69, no. 5 (May 1998): 2141–46. http://dx.doi.org/10.1063/1.1148913.

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33

Klausner, Arthur. "DuPont's DNA Sequencer Uses New Chemistry." Nature Biotechnology 5, no. 11 (November 1987): 1111–12. http://dx.doi.org/10.1038/nbt1187-1111.

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34

Eldon, John, and Rich Wegner. "Using the TMC2301 image resampling sequencer." Microprocessors and Microsystems 14, no. 2 (March 1990): 107–18. http://dx.doi.org/10.1016/0141-9331(90)90146-m.

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35

Evans, T. "Developing and commercializing a DNA sequencer." IEEE Engineering in Medicine and Biology Magazine 19, no. 4 (July 2000): 117–20. http://dx.doi.org/10.1109/51.853489.

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36

McCartney, David L. "Dual Camera Sequencer for Microsurgical Documentation." Ophthalmic Surgery, Lasers and Imaging Retina 21, no. 12 (December 1990): 860–61. http://dx.doi.org/10.3928/1542-8877-19901201-14.

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37

Hardman, Leigh, and Vincent Murray. "Use of an automated sequencer to determine the sequence specificity of DNA damage." IUBMB Life 42, no. 2 (June 1997): 349–59. http://dx.doi.org/10.1080/15216549700202751.

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38

Bailey, J. M., M. Rusnak, and J. E. Shively. "Compact Protein Sequencer for the C-Terminal Sequence Analysis of Peptides and Proteins." Analytical Biochemistry 212, no. 2 (August 1993): 366–74. http://dx.doi.org/10.1006/abio.1993.1342.

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39

GLÄSNER, Wolfgang, Rainer MERKL, Sabine SCHMIDT, Dieter CECH, and Hans-Joachim FRITZ. "Fast Quantitative Assay of Sequence-Specific Endonuclease Activity Based on DNA Sequencer Technology." Biological Chemistry Hoppe-Seyler 373, no. 2 (January 1992): 1223–26. http://dx.doi.org/10.1515/bchm3.1992.373.2.1223.

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40

Rahemi, Alireza, Thomas M. Gradziel, Jose X. Chaparro, Kevin M. Folta, Toktam Taghavi, Reza Fatahi, Ali Ebadi, and Darab Hassani. "Phylogenetic relationships among the first and second introns of selected Prunus S-RNase genes." Canadian Journal of Plant Science 95, no. 6 (November 2015): 1145–54. http://dx.doi.org/10.4141/cjps-2015-102.

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Rahemi, A., Gradziel T.M., Chaparro J.X., Folta, K.M., Taghavi, T., Fatahi, R., Ebadi, A. and Hassani, D. 2015. Phylogenetic relationships among the first and second introns of selected Prunus S-RNase genes. Can. J. Plant Sci. 95: 1145–1154. To identify and evaluate self-incompatible alleles in almonds and related germplasm, DNA from 15 Prunus species was amplified using two degenerate consensus primer pairs flanking first and second S-locus introns (PaConsI-FD+EM-Pc1ConsRD and EM-Pc2ConsFD+EM-Pc3ConsRD). Twenty-eight amplified PCR products were analyzed by automated sequencer capillary electr

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41

Keijser, B. J. F., E. Zaura, S. M. Huse, J. M. B. M. van der Vossen, F. H. J. Schuren, R. C. Montijn, J. M. ten Cate, and W. Crielaard. "Pyrosequencing analysis of the Oral Microflora of healthy adults." Journal of Dental Research 87, no. 11 (November 2008): 1016–20. http://dx.doi.org/10.1177/154405910808701104.

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A good definition of commensal microflora and an understanding of its relation to health are essential in preventing and combating disease. We hypothesized that the species richness of human oral microflora is underestimated. Saliva and supragingival plaque were sampled from 71 and 98 healthy adults, respectively. Amplicons from the V6 hypervariable region of the small-subunit ribosomal RNA gene were generated by PCR, pooled into saliva and plaque pools, and sequenced by means of the Genome Sequencer 20 system at 454 Life Sciences. Data were evaluated by taxonomic and rarefaction analyses. The

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42

FUKANO, Yoshihito, Yuki MIYAZAWA, Taiju MIKOSHI, Toshio INOUE, Shuuichirou MARUOKA, Kazumichi KURODA, Yasuhiro GON, Shu HASHIMOTO, and Kenji YAMAGISHI. "RNA-Sequence Analysis by Next-Generation Sequencer for the Early Diagnosis of Respiratory Disease." Journal of Computer Chemistry, Japan 13, no. 6 (2015): 332–34. http://dx.doi.org/10.2477/jccj.2014-0054.

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43

Shibata, K. "RIKEN Integrated Sequence Analysis (RISA) System---384-Format Sequencing Pipeline with 384 Multicapillary Sequencer." Genome Research 10, no. 11 (November 1, 2000): 1757–71. http://dx.doi.org/10.1101/gr.152600.

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44

Kamahori, Masao, Satoshi Takahashi, and Hideki Kambara. "Multi-capillary DNA sequencer and its applications." SEIBUTSU BUTSURI KAGAKU 41, no. 6 (1997): 313–18. http://dx.doi.org/10.2198/sbk.41.313.

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45

Rothstein, Joseph. "Voyetra Sequencer Plus Gold for IBM PCs." Computer Music Journal 15, no. 3 (1991): 124. http://dx.doi.org/10.2307/3680778.

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46

Roberts, Arthur. "Steinberg-Jones CUBASE Sequencer for Atari Computers." Computer Music Journal 15, no. 4 (1991): 128. http://dx.doi.org/10.2307/3681095.

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47

Mendoza, Edgar A., Alexander Neumann, Yuliya Kuznetsova, Steve R. J. Brueck, and Jeremy Edwards. "[INVITED] Electrophoretic plasmonic nanopore biochip genome sequencer." Optics & Laser Technology 109 (January 2019): 199–211. http://dx.doi.org/10.1016/j.optlastec.2018.07.011.

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48

Chiakang Sung, P. T. Sasaki, R. Leung, Yuet-Ming Chu, K. M. Le, G. W. Conner, R. H. Lane, J. L. De Jong, and R. Cline. "A 76-MHz BiCMOS programmable logic sequencer." IEEE Journal of Solid-State Circuits 24, no. 5 (October 1989): 1287–94. http://dx.doi.org/10.1109/jssc.1989.572598.

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49

Hosseini, Mahdi, Ben M. Sparkes, Gabriel Hétet, Jevon J. Longdell, Ping Koy Lam, and Ben C. Buchler. "Coherent optical pulse sequencer for quantum applications." Nature 461, no. 7261 (September 2009): 241–45. http://dx.doi.org/10.1038/nature08325.

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50

Check Hayden, Erika. "Pint-sized DNA sequencer impresses first users." Nature 521, no. 7550 (May 2015): 15–16. http://dx.doi.org/10.1038/521015a.

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