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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 RCRRH. This sequence has a calculated molecular weight of 6674 and is homologous with four other published mammalian protamine sequences.

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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. In this review, we mainly focus on base modification detection in the DNA and RNA of mammals using the Nanopore sequencer. We summarize current studies of modifications using the Nanopore sequencer, detection tools using statistical tests or machine learning, and applications of this technology, such as analyses of open chromatin, DNA replication, and RNA metabolism.

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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 throughput of samples. Secondly, polar amino acids such as phosphoserine, and polar derivatives formed by active-site photoaffinity labelling with 8-azido-ATP, are recovered quantitatively from the reaction column and can be positively identified. In other types of sequencer these polar derivatives, being somewhat insoluble in butyl chloride, tend to remain in the reaction chamber of the instrument and so are more difficult to identify. The solid-phase protein sequencer is also more suited than the liquid-phase instrument for analysis of proteolipids from membranes. These hydrophobic proteins tend to dissolve in organic solvents during washing steps in the liquid-phase instrument and are lost. Covalent attachment as used in the solid-phase instrument solves this problem.

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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 alignment matrix computation finished. Therefore, a new technique, known as overlap computation and configuration (OCC) is proposed to minimize the time overhead for performing biological sequence alignment. The OCC technique simultaneously updating substitution matrix in a processing element (PE) systolic array, while computing alignment matrix scores. Results showed that, the sequencer achieves more than two order of magnitude speed-up higher compared to the state of the art, at negligible area overhead, if any.

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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 sequencing was performed in A. agrarius lung tissues collected from the Republic of Korea. Genomic sequences of HTNV were analyzed based on the viral RNA copy numbers. Amplicon-based nanopore sequencing provided nearly full-length genomic sequences of HTNV and showed sufficient read depth for phylogenetic analysis after 8 h of sequencing. The average identity of the HTNV genome sequences for the nanopore sequencer compared to those of generated from Illumina MiSeq revealed 99.8% (L and M segments) and 99.7% (S segment) identities, respectively. This study highlights the potential of the portable nanopore sequencer for rapid generation of accurate genomic sequences of HTNV for quicker decision making in point-of-care testing of HFRS patients during a hantavirus outbreak.

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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, and Masato Suzuki. "Plasmid analysis of NDM metallo-β-lactamase-producing Enterobacterales isolated in Vietnam." PLOS ONE 16, no. 7 (July 28, 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 Enterobacterales isolated in Vietnam, and identified several possible cases of horizontal transfer of plasmids both within and among species of bacteria. Twenty-five carbapenem-nonsusceptible isolates from a medical institution in Hanoi were sequenced on Illumina short-read sequencers, and 13 blaNDM-positive isolates, including isolates of Klebsiella pneumoniae, Escherichia coli, Citrobacter freundii, Morganella morganii, and Proteus mirabilis, were further sequenced on an Oxford Nanopore Technologies long-read sequencer to obtain complete plasmid sequences. Almost identical 73 kb IncFII(pSE11)::IncN hybrid plasmids carrying blaNDM-1 were found in a P. mirabilis isolate and an M. morganii isolate. A 112 kb IncFII(pRSB107)::IncN hybrid plasmid carrying blaNDM-1 in an E. coli isolate had partially identical sequences with a 39 kb IncR plasmid carrying blaNDM-1 and an 88 kb IncFII(pHN7A8)::IncN hybrid plasmid in a C. freundii isolate. 148–149 kb IncFIA(Hl1)::IncA/C2 plasmids and 75–76 kb IncFII(Yp) plasmids, both carrying blaNDM-1 were shared among three sequence type 11 (ST11) isolates and three ST395 isolates of K. pneumoniae, respectively. Most of the plasmids co-carried genes conferring resistance to clinically relevant antimicrobials, including third-generation cephalosporins, aminoglycosides, and fluoroquinolones, in addition to blaNDM-1. These results provide insight into the genetic basis of CRE in Vietnam, and could help control nosocomial infections.

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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 correctly identify viral presence and species using BLAST, though direct RNA reads were more frequently misassigned to closely related CHV species. De novo consensus sequences were error prone but suitable for viral species identification. However, subtype identification was less accurate from both reads and consensus sequences. This is due to the high sequencing error rate and the limited sequence divergence between some CHV-1 subtypes. Importantly, neither RNA nor amplicon sequencing reads could be used to obtain reliable intra-host variants. Overall, both sequencing techniques were suitable for virus detection, though limitations are present due to the error rate of MinION reads.

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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 resolved according to peptide size by gel filtration on Sephadex LH60 in formic acid:ethanol. The position of 3H-labeled palmitoylated amino acids in peptides could not be identified by analysis of the Edman degradation sequencer product because the palmitoylated sequencer products were lost during the final derivatization step to phenylthiohydantoin derivatives. Modification of the gas/liquid-phase sequencer to deliver the intermediate anilinothiozolinone derivative, rather than the phenylthiohydantoin derivative, identified the cycle containing the 3H-labeled palmitoylated residue. Therefore, structure analysis of peptides obtained from gel filtration necessitated dual sequencer runs of radioactive peptides, one for sequence analysis and one to identify 3H-labeled palmitoylated amino acids. Further cleavage of the CNBr peptides by trypsin and Lys-C protease, followed by gel filtration on Sephadex LH60 and dual sequencer runs, positioned the 3H-labeled palmitoylated amino acid residues in peptides. Integration of all the available structural information led to the assignment of the palmitoyl moiety to specific residues in alpha-tubulin. The palmitoylated residues in alpha-tubulin were confined to cysteine residues only. The major site for palmitoylation was cysteine residue 376.

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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. Objective.—To demonstrate the fundamental principles of pyrosequencing. Data Sources.—Salient features of pyrosequencing are demonstrated using the free software program Pyromaker (http://pyromaker.pathology.jhmi.edu), through which users can input DNA sequences and other pyrosequencing parameters to generate the expected pyrosequencing results. Conclusions.—We demonstrate how mutant and wild-type DNA sequences result in different pyrograms. Using pyrograms of established mutations in tumors, we explain how to analyze the pyrogram peaks generated by different dispensation sequences. Further, we demonstrate some limitations of pyrosequencing, including how some complex mutations can be indistinguishable from single base mutations. Pyrosequencing is the basis of the Roche 454 next-generation sequencer and many of the same principles also apply to the Ion Torrent hydrogen ion-based next-generation sequencers.

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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 assembly, pairwise single nucleotide polymorphisms (SNPs) were determined. The plasmids were annotated, and a pan-genome was constructed to compare genes variably present between the different plasmids. Nine Escherichia coli sequences of broiler origin, four Escherichia coli sequences, and one Salmonella enterica sequence of human origin were selected for the current analysis. A circular contig with the IncI1–pST12 replicon and blaCMY-2 gene was extracted from the assembly graph of all fourteen isolates. Analysis of the IncI1–pST12 plasmids revealed a low number of SNP differences (range of 0–9 SNPs). The range of SNP differences overlapped in isolates with different epidemiological links. One-hundred and twelve from a total of 113 genes of the pan-genome were present in all plasmid constructs. Next generation sequencing analysis of blaCMY-2-containing IncI1–pST12 plasmids isolated from Enterobacteriaceae with different epidemiological links show a high degree of sequence similarity in terms of SNP differences and the number of shared genes. Therefore, statements on the horizontal transfer of these plasmids based on genetic identity should be made with caution.

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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 abundance. Despite high error rates, highly accurate consensus sequences can be derived. This methodological approach identified all mock community taxa, demonstrating the MinION can be used as a practical alternative to profile fungal communities.

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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. algivorus, V. casei, V. litoralis, and V. rumoiensis. Comparison of overall genome relatedness indices (OGRI) and multilocus sequence analysis (MLSA) based on Nanopore-only assembly and Illumina or hybrid assemblies revealed that errors in Nanopore-only assembly do not influence average nucleotide identity (ANI), in silico DNA-DNA hybridization (DDH), G+C content, or MLSA tree topology in Vibrionaceae. Our results show that the genome sequences from Nanopore-based approach can be used for rapid species identification based on the OGRI and MLSA.

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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 channel devoted to updates to and analysis of nanopore sequence data.

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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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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 electrophoresis. Sequenced fragments were aligned against available Prunus S-locus sequences in the National Center for Biotechnology Information and S-alleles identities were determined. The phylogenetic relationships between S-alleles in the germplasm studied were determined by the homology between their sequences and dendrograms were obtained for each primer pair. The Maximum Likelihood (homology) ranged from 84 to 100%. Most sequences were similar to cultivated almond (Prunus dulcis) or to the European wild almond (P. webbii). Twenty-six alleles for the first and the second introns were registered in the database in the GenBank. Two sequences of the first and second introns, which were taken from Prunus nairica and had similarity in GenBank, were registered in the database under a common sequence of the first and second intron. Analysis of phylogenetic relationships (dendrograms) among S-alleles from wild almond species as well as S-alleles cluster relations showed most pairs of alleles well supported by bootstrap.

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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 197,600 sequences generated yielded about 29,000 unique sequences, representing 22 taxonomic phyla. Grouping the sequences in operational taxonomic units (6%) yielded 3621 and 6888 species-level phylotypes in saliva and plaque, respectively. This work gives a radically new insight into the diversity of human oral microflora, which, with an estimated number of 19,000 phylotypes, is considerably higher than previously reported.

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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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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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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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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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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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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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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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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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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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