Journal articles: 'Sequences'

1

He, Tian-Xiao. "A-sequences, Z-sequence, and B-sequences of Riordan matrices." Discrete Mathematics 343, no. 3 (March 2020): 111718. http://dx.doi.org/10.1016/j.disc.2019.111718.

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Leng, Rhodri, Gil Viry, Miguel García-Sancho, James Lowe, Mark Wong, and Niki Vermeulen. "The Sequences and the Sequencers." Historical Studies in the Natural Sciences 52, no. 3 (June 1, 2022): 277–319. http://dx.doi.org/10.1525/hsns.2022.52.3.277.

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This special issue on sequences and sequencers uses new analytical approaches to re-assess the history of genomics. Historical attention has largely focused on a few central characters and institutions: those that participated in the Human Genome Project (HGP), especially its final stages. Our analysis—based on an assessment of almost 13.5 million DNA sequence submissions and 30,000 publications of human, yeast, and pig DNA sequences—followed overlapping chronologies starting before and finishing after the concerted efforts to sequence the genomes of each species: 1980 to 2000 in yeast, 1985 to 2005 for the human, and 1990 to 2015 for the pig. Our main conclusion is that when broader sequencing practices—especially those addressed to nonhuman species—are taken into account, the large-scale center model that characterized the organization of the HGP falls short in representing genomics as a whole. Instead of taking the HGP as a model, we describe an iterative process in which the practices of sequence submission and publication were entangled. Analysis of co-authorship networks between institutions derived from our data shows how linked sequence submission and publication were to medical, biochemical, and agricultural research. Our analysis thus reveals the utility of big data and mixed-methods approaches for addressing science as a multidimensional endeavor with a history shaped by co-constitutive, synchronic interactions among different elements—such as communities, species, and disciplines—as much as diachronic trajectories over time. This perspective enables us to better capture interdisciplinary and interspecies work, and offers a more fluid portrayal of the connections between scientific practices and agricultural, industrial, and medical goals. This essay is part of a special issue entitled The Sequences and the Sequencers: A New Approach to Investigating the Emergence of Yeast, Human, and Pig Genomics, edited by Michael García-Sancho and James Lowe.

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3

Sanger, Frederick. "Sequences, Sequences, and Sequences." Annual Review of Biochemistry 57, no. 1 (June 1988): 1–29. http://dx.doi.org/10.1146/annurev.bi.57.070188.000245.

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4

He, Ping-an, and Jun Wang. "Characteristic Sequences for DNA Primary Sequence." Journal of Chemical Information and Computer Sciences 42, no. 5 (September 2002): 1080–85. http://dx.doi.org/10.1021/ci010131z.

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5

Enkosky, Thomas, and Branden Stone. "A sequence defined by M-sequences." Discrete Mathematics 333 (October 2014): 35–38. http://dx.doi.org/10.1016/j.disc.2014.06.007.

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6

Velhagen, William A. "Analyzing Developmental Sequences Using Sequence Units." Systematic Biology 46, no. 1 (March 1, 1997): 204–10. http://dx.doi.org/10.1093/sysbio/46.1.204.

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7

Tatum, Zuotian, Marco Roos, Andrew P. Gibson, Peter EM Taschner, Mark Thompson, Erik A. Schultes, and Jeroen FJ Laros. "Preserving sequence annotations across reference sequences." Journal of Biomedical Semantics 5, Suppl 1 (2014): S6. http://dx.doi.org/10.1186/2041-1480-5-s1-s6.

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8

Tsai, Lu, Liaofu Luo, and Zhirong Sun. "Sequence-Dependent Flexibility in Promoter Sequences." Journal of Biomolecular Structure and Dynamics 20, no. 1 (August 2002): 127–34. http://dx.doi.org/10.1080/07391102.2002.10506828.

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9

Hanage, William P., Christophe Fraser, and Brian G. Spratt. "Sequences, sequence clusters and bacterial species." Philosophical Transactions of the Royal Society B: Biological Sciences 361, no. 1475 (October 6, 2006): 1917–27. http://dx.doi.org/10.1098/rstb.2006.1917.

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Whatever else they should share, strains of bacteria assigned to the same species should have house-keeping genes that are similar in sequence. Single gene sequences (or rRNA gene sequences) have very few informative sites to resolve the strains of closely related species, and relationships among similar species may be confounded by interspecies recombination. A more promising approach (multilocus sequence analysis, MLSA) is to concatenate the sequences of multiple house-keeping loci and to observe the patterns of clustering among large populations of strains of closely related named bacterial species. Recent studies have shown that large populations can be resolved into non-overlapping sequence clusters that agree well with species assigned by the standard microbiological methods. The use of clustering patterns to inform the division of closely related populations into species has many advantages for poorly studied bacteria (or to re-evaluate well-studied species), as it provides a way of recognizing natural discontinuities in the distribution of similar genotypes. Clustering patterns can be used by expert groups as the basis of a pragmatic approach to assigning species, taking into account whatever additional data are available (e.g. similarities in ecology, phenotype and gene content). The development of large MLSA Internet databases provides the ability to assign new strains to previously defined species clusters and an electronic taxonomy. The advantages and problems in using sequence clusters as the basis of species assignments are discussed.

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10

Burzyk, Jósef. "On $K$-sequences." Czechoslovak Mathematical Journal 43, no. 1 (1993): 1–6. http://dx.doi.org/10.21136/cmj.1993.128383.

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11

Clarke, Neil D. "Sequence ‘minimization’: exploring the sequence landscape with simplified sequences." Current Opinion in Biotechnology 6, no. 4 (January 1995): 467–72. http://dx.doi.org/10.1016/0958-1669(95)80077-8.

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12

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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13

Liu, Zhi-Hua, Dian Jiao, and Xiao Sun. "Classifying Genomic Sequences by Sequence Feature Analysis." Genomics, Proteomics & Bioinformatics 3, no. 4 (2005): 201–5. http://dx.doi.org/10.1016/s1672-0229(05)03027-5.

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14

Valiquette, G., E. A. Zimmerman, and J. L. Roberts. "mRNA sequence predictions from homologous protein sequences." Journal of Theoretical Biology 112, no. 3 (February 1985): 445–58. http://dx.doi.org/10.1016/s0022-5193(85)80013-8.

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15

Ural, Hasan, and Zhiping Wang. "Synchronizable test sequence generation using UIO sequences." Computer Communications 16, no. 10 (October 1993): 653–61. http://dx.doi.org/10.1016/0140-3664(93)90082-4.

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16

Gomez, John, and Rafael Jimenez. "Sequence, a BioJS component for visualising sequences." F1000Research 3 (February 13, 2014): 52. http://dx.doi.org/10.12688/f1000research.3-52.v1.

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Summary: Sequences are probably the most common piece of information in sites providing biological data resources, particularly those related to genes and proteins. Multiple visual representations of the same sequence can be found across those sites. This can lead to an inconsistency compromising both the user experience and usability while working with graphical representations of a sequence. Furthermore, the code of the visualisation module is commonly embedded and merged with the rest of the application, making it difficult to reuse it in other applications. In this paper, we present a BioJS component for visualising sequences with a set of options supporting a flexible configuration of the visual representation, such as formats, colours, annotations, and columns, among others. This component aims to facilitate a common representation across different sites, making it easier for end users to move from one site to another.Availability: http://www.ebi.ac.uk/Tools/biojs; http://dx.doi.org/10.5281/zenodo.8299

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17

Garcia, Adriana, María José Muñoz Torrecillas, and Salvador Cruz Rambaud. "The improving sequence effect on monetary sequences." Heliyon 6, no. 12 (December 2020): e05643. http://dx.doi.org/10.1016/j.heliyon.2020.e05643.

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18

Savaş, Ekrem, and Richard F. Patterson. "Double sequence spaces characterized by lacunary sequences." Applied Mathematics Letters 20, no. 9 (September 2007): 964–70. http://dx.doi.org/10.1016/j.aml.2006.09.008.

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19

Hassaan, Mosab. "Classification Event Sequences via Compact Big Sequence." Kafrelsheikh Journal of Information Sciences 3, no. 2 (December 1, 2022): 1–9. http://dx.doi.org/10.21608/kjis.2022.181419.1012.

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20

Fatchiyah, Fatchiyah, Rista Nikmatu Rohmah, Lidwina Faraline Tripisila, Dewi Ratih Tirto Sari, Adelia Adrianne Tapiory, Jihan Safira Ainnayah, Viona Faiqoh, Fajar Mustika Alam, and Ahmad Faizal Abdul Razis. "Three-dimension Glyceraldehyde-3-Phosphate Dehydrogenase protein structure of substitution and insertion sequences of GAPDH gene of chicken drumstick meat (Gallus gallus)." Berkala Penelitian Hayati 27, no. 2 (April 5, 2022): 105–9. http://dx.doi.org/10.23869/bphjbr.27.2.20228.

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The study aimed to observed the 3-D structure of GAPDH protein and identify the GAPDH gene sequences mutation of chicken drumstick meat (Gallus gallus). The sample of chicken meat was randomly taken in four districts in Malang city. In this study, the DNA was isolated from drumstick meat chicken samples, amplified using proper primers, and then sequenced using ABI 3730xl DNA Sequencer. The DNA sequences alignments analyzed by BioEdit software and the control sequence of GAPDH gene was obtained from NCBI GenBank (sequence Gene ID: 374193). Then, the amino acid sequence and 3D structure of GAPDH protein were determined based on the change of nucleotide sequences using Swiss model and PyMol software. The nucleotide sequence of a partially GAPDH gene of drumstick meat chicken from districts two is completely different with a 97 percent similarity level, which found twelve nucleotides’ substitutions mutation between nucleotide base number 354 until 777 and three nucleotides inserted between T753 and G754 nucleotide base. These mutations changed the amino acid sequence and 3D structure of GAPDH protein. This result suggests that the differential drumstick chicken meat GAPDH sequences and 3D structure may induce the change of protein-protein interaction and induction.

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21

Kiebel, Stefan J., Katharina von Kriegstein, Jean Daunizeau, and Karl J. Friston. "Recognizing Sequences of Sequences." PLoS Computational Biology 5, no. 8 (August 14, 2009): e1000464. http://dx.doi.org/10.1371/journal.pcbi.1000464.

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22

SHAN, YING, HARPREET S. SAWHNEY, and ART POPE. "CLUSTERING MULTIPLE IMAGE SEQUENCES WITH A SEQUENCE-TO-SEQUENCE SIMILARITY MEASURE." International Journal of Pattern Recognition and Artificial Intelligence 19, no. 04 (June 2005): 551–64. http://dx.doi.org/10.1142/s0218001405004149.

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We propose a novel similarity measure of two image sequences based on shapeme histograms. The idea of shapeme histogram has been used for single image/texture recognition, but is used here to solve the sequence-to-sequence matching problem. We develop techniques to represent each sequence as a set of shapeme histograms, which captures different variations of the object appearances within the sequence. These shapeme histograms are computed from the set of 2D invariant features that are stable across multiple images in the sequence, and therefore minimizes the effect of both background clutter, and 2D pose variations. We define sequence similarity measure as the similarity of the most similar pair of images from both sequences. This definition maximizes the chance of matching between two sequences of the same object, because it requires only part of the sequences being similar. We also introduce a weighting scheme to conduct an implicit feature selection process during the matching of two shapeme histograms. Experiments on clustering image sequences of tracked objects demonstrate the efficacy of the proposed method.

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23

Seidman, Thomas I. "On certain iterative sequences." Časopis pro pěstování matematiky 112, no. 2 (1987): 162–72. http://dx.doi.org/10.21136/cpm.1987.118304.

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24

Sodin, Sasha. "Fluctuations of Interlacing Sequences." Zurnal matematiceskoj fiziki, analiza, geometrii 13, no. 4 (December 25, 2017): 364–401. http://dx.doi.org/10.15407/mag13.04.364.

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25

Thanh, Tran Tan, Hoang Minh Tu Van, Nguyen Thi Thu Hong, Le Nguyen Truc Nhu, Nguyen To Anh, Ha Manh Tuan, Ho Van Hien, et al. "The first genome sequences of human bocaviruses from Vietnam." Wellcome Open Research 1 (November 16, 2016): 16. http://dx.doi.org/10.12688/wellcomeopenres.10042.1.

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As part of an ongoing effort to generate complete genome sequences of hand, foot and mouth disease-causing enteroviruses directly from clinical specimens, two complete coding sequences and two partial genomic sequences of human bocavirus 1 (n=3) and 2 (n=1) were co-amplified and sequenced, representing the first genome sequences of human bocaviruses from Vietnam. The sequences may aid future study aiming at understanding the evolution of the pathogen.

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26

Thanh, Tran Tan, Hoang Minh Tu Van, Nguyen Thi Thu Hong, Le Nguyen Truc Nhu, Nguyen To Anh, Ha Manh Tuan, Ho Van Hien, et al. "The first genome sequences of human bocaviruses from Vietnam." Wellcome Open Research 1 (January 9, 2017): 16. http://dx.doi.org/10.12688/wellcomeopenres.10042.2.

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As part of an ongoing effort to generate complete genome sequences of hand, foot and mouth disease-causing enteroviruses directly from clinical specimens, two complete coding sequences and two partial genomic sequences of human bocavirus 1 (n=3) and 2 (n=1) were co-amplified and sequenced, representing the first genome sequences of human bocaviruses from Vietnam. The sequences may aid future study aiming at understanding the evolution of the virus.

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27

Wu, Fone-Mao, and Peter M. Muriana. "Cloning, Sequencing, and Characterization of Genomic Subtracted Sequences from Listeria monocytogenes." Applied and Environmental Microbiology 65, no. 12 (December 1, 1999): 5427–30. http://dx.doi.org/10.1128/aem.65.12.5427-5430.1999.

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ABSTRACT Individual sequences of a genomic subtracted, PCR-amplified, mixed-sequence probe (GS probe) were cloned and sequenced. The GS probe differentiated restriction fragment length polymorphism patterns forListeria monocytogenes but did not hybridize with members of other bacterial genera. Sequence analysis identified severalL. monocytogenes sequences already present in the GenBank database; the putative identities of other sequences were inferred from homology data, and still other sequences did not exhibit significant levels of homology with any GenBank sequences.

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28

Cummings, James. "Coherent sequences versus Radin sequences." Annals of Pure and Applied Logic 70, no. 3 (December 1994): 223–41. http://dx.doi.org/10.1016/s0168-0072(94)90010-8.

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29

Fishburn, Peter C., and Fred S. Roberts. "Elementary sequences, sub-Fibonacci sequences." Discrete Applied Mathematics 44, no. 1-3 (July 1993): 261–81. http://dx.doi.org/10.1016/0166-218x(93)90236-h.

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30

Eggleton, Roger B., Aviezri S. Fraenkel, and R. Jaime Simpson. "Beatty sequences and Langford sequences." Discrete Mathematics 111, no. 1-3 (February 1993): 165–78. http://dx.doi.org/10.1016/0012-365x(93)90153-k.

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31

Ahlswede, Rudolf, Levon Khachatrian, and András Sárközy. "On the quotient sequence of sequences of integers." Acta Arithmetica 91, no. 2 (1999): 117–32. http://dx.doi.org/10.4064/aa-91-2-117-132.

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32

Truong, Dang Van, and Le Chi Quynh. "Applying M-sequences Decimation to Generate Interleaved Sequence." Journal of Science and Technology on Information security 2, no. 14 (January 14, 2022): 75–80. http://dx.doi.org/10.54654/isj.v2i14.207.

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Abstract—M-sequences are widely used in for many purposes, from synchronization, whitening, communications and cryptography. We analyze decimation techniques and introduce two methods to generate decimation sequences which don’t have to calculate intermediate states. Then we apply these methods to interleaved sequence as a new method to pre-calculate for set of interleaved order which is more effective in implementation. Tóm tắt—M-dãy đang được sử dụng rất rộng rãi trong nhiều lĩnh vực, từ việc đồng bộ, làm trắng thông tin, viễn thông và kỹ thuật mật mã. Chúng tôi phân tích kỹ thuật phân rã m-dãy theo bước và giới thiệu hai phương pháp sinh dãy phân rã theo bước mà không cần tính các trạng thái trung gian. Áp dụng phương pháp này vào dãy lồng ghép, ta có một phương pháp mới để tính trước tập các thứ tự lồng ghép có tính hiệu quả trong cài đặt thực tế.

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33

Courville, P., and P. Y. Collin. "Taphonomic sequences—A new tool for sequence stratigraphy." Geology 30, no. 6 (2002): 511. http://dx.doi.org/10.1130/0091-7613(2002)030<0511:tsantf>2.0.co;2.

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34

Doolittle, Russell F. "Protein sequence comparisons: searching databases and aligning sequences." Current Opinion in Biotechnology 5, no. 1 (February 1994): 24–28. http://dx.doi.org/10.1016/s0958-1669(05)80065-5.

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35

Koonin, Eugene V. "Genome sequences: Genome sequence of a model prokaryote." Current Biology 7, no. 10 (October 1997): R656—R659. http://dx.doi.org/10.1016/s0960-9822(06)00328-9.

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36

Andersson, Per M., Michael Sjöström, and Torbjörn Lundstedt. "Preprocessing peptide sequences for multivariate sequence-property analysis." Chemometrics and Intelligent Laboratory Systems 42, no. 1-2 (August 1998): 41–50. http://dx.doi.org/10.1016/s0169-7439(98)00062-8.

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37

Churchill, Gary A., and Michael S. Waterman. "The accuracy of DNA sequences: Estimating sequence quality." Genomics 14, no. 1 (September 1992): 89–98. http://dx.doi.org/10.1016/s0888-7543(05)80288-5.

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38

Galy, Edith, Jean-François Camps, and Claudine Melan. "Sequence Class Formation Following Learning of Short Sequences." Psychological Record 53, no. 4 (October 2003): 635–45. http://dx.doi.org/10.1007/bf03395457.

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39

Ural, H., and K. Zhu. "Optimal length test sequence generation using distinguishing sequences." IEEE/ACM Transactions on Networking 1, no. 3 (June 1993): 358–71. http://dx.doi.org/10.1109/90.234857.

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40

Qi, Feng, and Bai-Ni Guo. "Monotonicity of sequences involving convex function and sequence." Mathematical Inequalities & Applications, no. 2 (2006): 247–54. http://dx.doi.org/10.7153/mia-09-25.

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41

Tripathy, Binod Chandra, and Bipan Hazarika. "I-convergent sequence spaces associated with multiplier sequences." Mathematical Inequalities & Applications, no. 3 (2008): 543–48. http://dx.doi.org/10.7153/mia-11-43.

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42

Hammen, Philip K., and Henry Weiner. "Mitochondrial leader sequences: Structural similarities and sequence differences." Journal of Experimental Zoology 282, no. 1-2 (September 1998): 280–83. http://dx.doi.org/10.1002/(sici)1097-010x(199809/10)282:1/2<280::aid-jez30>3.0.co;2-v.

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43

He, Ping-an, and Jun Wang. "ChemInform Abstract: Characteristic Sequences for DNA Primary Sequence." ChemInform 33, no. 47 (May 19, 2010): no. http://dx.doi.org/10.1002/chin.200247209.

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44

Wang, Ke, Jiuyu Hao, Lei Wang, and Huimin Li. "Phase factor sequences algorithm in partial transmit sequence." Transactions of Tianjin University 15, no. 1 (February 2009): 23–26. http://dx.doi.org/10.1007/s12209-009-0005-6.

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45

Lüke, Hans Dieter, and Hafez Hadinejad-Mahram. "Sequences and sequence pairs with imaginary correlation sidelobes." European Transactions on Telecommunications 15, no. 5 (September 2004): 485–90. http://dx.doi.org/10.1002/ett.995.

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46

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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Artimová, Renata, Lukáš Hleba, Soňa Javoreková, Jana Maková, Janka Medová, and Juraj Medo. "CHLOROPLAST EXCLUDING PRIMERS FOR METAGENOMIC ANALYSIS OF BACTERIA IN PLANT TISSUES." Journal of microbiology, biotechnology and food sciences 12, no. 3 (November 30, 2022): e9650. http://dx.doi.org/10.55251/jmbfs.9650.

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Plant microbiomes are responsible for the growth, health, nutrition, and resistance to biotic and abiotic stress. Moreover, some plant microbiome members, especially the Enterobacteriaceae family, can act as human pathogens. In recent years, metagenomic analysis of amplified 16S rRNA gene sequenced on Illumina second generation sequencers became the most widely used method for bacterial microbiome studies. The 16S r RNA gene of the bacterium is phylogenetically similar to the 16S genes of chloroplasts and mitochondria since they have common prokaryotic ancestors. Thus, plant microbiome analysis is affected by unwanted non-target chloroplast and mitochondrial sequences. The solution to this contamination uses specially designed primer pairs that exclude chloroplasts and mitochondria and provide undistorted information. In this study, we analyzed chloroplast excluding primer 799R (reverse complement of 799F) which contains 4 mismatches of nucleotides against the chloroplast sequence modified for use with Illumina sequencers. We used primer 799R with universal bacterial forward primers 341F and 515F and compared the results obtained with 799R to the results obtained with the universal 806R primer. Microbiomes of 12 samples from 4 distinct parts of the tomato plants (Solanum lycopersicon L.) leaves, fruits, roots, and rhizosphere, were amplified using all combinations of these primers. The combination of universal forward primers 515F or 341F with the universal bacterial primer 806R amplified 60-85% of chloroplast sequences in samples of plant tissue. The 799R primer effectively reduced the number of chloroplast sequences to less than 1%. However, some sequences derived from mitochondria remained, with a higher proportion using the 341F primer (66-72%) than 515F (21-28%). The ability to describe microbial population diversity using 799R was similar to 806R, although there is a clear difference in the proportions of amplified microorganism groups using these primers. Analysis revealed the highest frequency of Enterobacteriaceae when primer pair 515F+799R was used. Based on the results, the combination of primers 515F+799R was the most appropriate, met all parameters, and can be recommended for routine analysis of plant microbiomes using second generation sequencers.

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48

Hamza Al Cheikha, Ahmad. "Compose Quotient Ring Sequences with Walsh’s Sequences and M-Sequences." International Journal of Theoretical and Applied Mathematics 5, no. 1 (2019): 10. http://dx.doi.org/10.11648/j.ijtam.20190501.12.

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49

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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Helal, Manal, Fanrong Kong, Sharon C.-A. Chen, Fei Zhou, Dominic E. Dwyer, John Potter, and Vitali Sintchenko. "Linear normalised hash function for clustering gene sequences and identifying reference sequences from multiple sequence alignments." Microbial Informatics and Experimentation 2, no. 1 (2012): 2. http://dx.doi.org/10.1186/2042-5783-2-2.

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Journal articles on the topic 'Sequences'

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