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Relevant bibliographies by topics / Sequence Analysis, DNA – methods

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Academic literature on the topic 'Sequence Analysis, DNA – methods'

Author: Grafiati

Published: 4 June 2021

Last updated: 8 February 2022

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Journal articles on the topic "Sequence Analysis, DNA – methods"

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Steinke, Dirk, Miguel Vences, Walter Salzburger, and Axel Meyer. "TaxI: a software tool for DNA barcoding using distance methods." Philosophical Transactions of the Royal Society B: Biological Sciences 360, no. 1462 (2005): 1975–80. http://dx.doi.org/10.1098/rstb.2005.1729.

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DNA barcoding is a promising approach to the diagnosis of biological diversity in which DNA sequences serve as the primary key for information retrieval. Most existing software for evolutionary analysis of DNA sequences was designed for phylogenetic analyses and, hence, those algorithms do not offer appropriate solutions for the rapid, but precise analyses needed for DNA barcoding, and are also unable to process the often large comparative datasets. We developed a flexible software tool for DNA taxonomy, named TaxI. This program calculates sequence divergences between a query sequence (taxon to be barcoded) and each sequence of a dataset of reference sequences defined by the user. Because the analysis is based on separate pairwise alignments this software is also able to work with sequences characterized by multiple insertions and deletions that are difficult to align in large sequence sets (i.e. thousands of sequences) by multiple alignment algorithms because of computational restrictions. Here, we demonstrate the utility of this approach with two datasets of fish larvae and juveniles from Lake Constance and juvenile land snails under different models of sequence evolution. Sets of ribosomal 16S rRNA sequences, characterized by multiple indels, performed as good as or better than cox1 sequence sets in assigning sequences to species, demonstrating the suitability of rRNA genes for DNA barcoding.

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McBride, L. J., S. M. Koepf, R. A. Gibbs, et al. "Automated DNA sequencing methods involving polymerase chain reaction." Clinical Chemistry 35, no. 11 (1989): 2196–201. http://dx.doi.org/10.1093/clinchem/35.11.2196.

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Abstract Polymerase chain reaction (PCR) as a method for preparing DNA templates has been used for several DNA sequencing applications. An in situ procedure for directly sequencing PCR products by the dideoxy-termination method has been developed by using fluorophore-labeled sequencing primers. Completed sequence reactions were combined and loaded into a single electrophoretic lane of a fluorescence-based DNA sequence analyzer. DNA targets devoid of a universal primer sequence could be sequenced with labeled universal primers by incorporating a universal primer sequence into the PCR product. With this method, the sequence of a 351-bp region in the bacteriophage lambda genome was fully analyzed in a single lane with automatic base identification accuracy of greater than 99%. An unknown sequence, 1.7 kb long, also was sequenced by this procedure, in combination with a "PCR gene walking" strategy. Comparison of the 1110 bases in overlapping sequence data from both strands yielded only two single-base ambiguities. Automated DNA sequence analysis of the highly polymorphic HLA-DQA-1 (alpha) region in the human genome can be performed with this simple methodology. Use of this PCR-sequencing method to analyze DNA extracted from a one-month-old blood sample from an individual who is heterozygous at this locus allowed unambiguous assignment of genotype.

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WILSON, R., and L. HOOD. "High-throughput fluorescent DNA sequence analysis: Methods and automation." Methods 3, no. 1 (1991): 48–54. http://dx.doi.org/10.1016/s1046-2023(05)80163-x.

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Matsuo, Kouki. "Evaluation of methods for plant genomic DNA sequence analysis without DNA and PCR product purification." Plant Science 312 (November 2021): 111023. http://dx.doi.org/10.1016/j.plantsci.2021.111023.

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Mendizabal-Ruiz, Gerardo, Israel Román-Godínez, Sulema Torres-Ramos, Ricardo A. Salido-Ruiz, Hugo Vélez-Pérez, and J. Alejandro Morales. "Genomic signal processing for DNA sequence clustering." PeerJ 6 (January 24, 2018): e4264. http://dx.doi.org/10.7717/peerj.4264.

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Genomic signal processing (GSP) methods which convert DNA data to numerical values have recently been proposed, which would offer the opportunity of employing existing digital signal processing methods for genomic data. One of the most used methods for exploring data is cluster analysis which refers to the unsupervised classification of patterns in data. In this paper, we propose a novel approach for performing cluster analysis of DNA sequences that is based on the use of GSP methods and the K-means algorithm. We also propose a visualization method that facilitates the easy inspection and analysis of the results and possible hidden behaviors. Our results support the feasibility of employing the proposed method to find and easily visualize interesting features of sets of DNA data.

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Gibson, Neil J. "The use of real-time PCR methods in DNA sequence variation analysis." Clinica Chimica Acta 363, no. 1-2 (2006): 32–47. http://dx.doi.org/10.1016/j.cccn.2005.06.022.

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Qi, Xingqin, Edgar Fuller, Qin Wu, and Cun-Quan Zhang. "Numerical Characterization of DNA Sequence Based on Dinucleotides." Scientific World Journal 2012 (2012): 1–6. http://dx.doi.org/10.1100/2012/104269.

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Sequence comparison is a primary technique for the analysis of DNA sequences. In order to make quantitative comparisons, one devises mathematical descriptors that capture the essence of the base composition and distribution of the sequence. Alignment methods and graphical techniques (where each sequence is represented by a curve in high-dimension Euclidean space) have been used popularly for a long time. In this contribution we will introduce a new nongraphical and nonalignment approach based on the frequencies of the dinucleotideXYin DNA sequences. The most important feature of this method is that it not only identifies adjacentXYpairs but also nonadjacentXYones whereXandYare separated by some number of nucleotides. This methodology preserves information in DNA sequence that is ignored by other methods. We test our method on the coding regions of exon-1 ofβ–globin for 11 species, and the utility of this new method is demonstrated.

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Stern, David B., Eduardo Castro Nallar, Jason Rathod, and Keith A. Crandall. "DNA Barcoding analysis of seafood accuracy in Washington, D.C. restaurants." PeerJ 5 (April 25, 2017): e3234. http://dx.doi.org/10.7717/peerj.3234.

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In Washington D.C., recent legislation authorizes citizens to test if products are properly represented and, if they are not, to bring a lawsuit for the benefit of the general public. Recent studies revealing the widespread phenomenon of seafood substitution across the United States make it a fertile area for consumer protection testing. DNA barcoding provides an accurate and cost-effective way to perform these tests, especially when tissue alone is available making species identification based on morphology impossible. In this study, we sequenced the 5′ barcoding region of the Cytochrome Oxidase I gene for 12 samples of vertebrate and invertebrate food items across six restaurants in Washington, D.C. and used multiple analytical methods to make identifications. These samples included several ambiguous menu listings, sequences with little genetic variation among closely related species and one sequence with no available reference sequence. Despite these challenges, we were able to make identifications for all samples and found that 33% were potentially mislabeled. While we found a high degree of mislabeling, the errors involved closely related species and we did not identify egregious substitutions as have been found in other cities. This study highlights the efficacy of DNA barcoding and robust analyses in identifying seafood items for consumer protection.

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Lu, Yue, Long Zhao, Zhao Li, and Xiangjun Dong. "Genetic Similarity Analysis Based on Positive and Negative Sequence Patterns of DNA." Symmetry 12, no. 12 (2020): 2090. http://dx.doi.org/10.3390/sym12122090.

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Similarity analysis of DNA sequences can clarify the homology between sequences and predict the structure of, and relationship between, them. At the same time, the frequent patterns of biological sequences explain not only the genetic characteristics of the organism, but they also serve as relevant markers for certain events of biological sequences. However, most of the aforementioned biological sequence similarity analysis methods are targeted at the entire sequential pattern, which ignores the missing gene fragment that may induce potential disease. The similarity analysis of such sequences containing a missing gene item is a blank. Consequently, some sequences with missing bases are ignored or not effectively analyzed. Thus, this paper presents a new method for DNA sequence similarity analysis. Using this method, we first mined not only positive sequential patterns, but also sequential patterns that were missing some of the base terms (collectively referred to as negative sequential patterns). Subsequently, we used these frequent patterns for similarity analysis on a two-dimensional plane. Several experiments were conducted in order to verify the effectiveness of this algorithm. The experimental results demonstrated that the algorithm can obtain various results through the selection of frequent sequential patterns and that accuracy and time efficiency was improved.

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Lipsky, Robert H., Chiara M. Mazzanti, Joseph G. Rudolph, et al. "DNA Melting Analysis for Detection of Single Nucleotide Polymorphisms." Clinical Chemistry 47, no. 4 (2001): 635–44. http://dx.doi.org/10.1093/clinchem/47.4.635.

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Abstract Background: Several methods for detection of single nucleotide polymorphisms (SNPs; e.g., denaturing gradient gel electrophoresis and denaturing HPLC) are indirectly based on the principle of differential melting of heteroduplex DNA. We present a method for detecting SNPs that is directly based on this principle. Methods: We used a double-stranded DNA-specific fluorescent dye, SYBR Green I (SYBR) in an efficient system (PE 7700 Sequence Detector) in which DNA melting was controlled and monitored in a 96-well plate format. We measured the decrease in fluorescence intensity that accompanied DNA duplex denaturation, evaluating the effects of fragment length, dye concentration, DNA concentration, and sequence context using four naturally occurring polymorphisms (three SNPs and a single-base deletion/insertion). Results: DNA melting analysis (DM) was used successfully for variant detection, and we also discovered two previously unknown SNPs by this approach. Concentrations of DNA amplicons were readily monitored by SYBR fluorescence, and DNA amplicon concentrations were highly reproducible, with a CV of 2.6%. We readily detected differences in the melting temperature between homoduplex and heteroduplex fragments 15–167 bp in length and differing by only a single nucleotide substitution. Conclusions: The efficiency and sensitivity of DMA make it highly suitable for the large-scale detection of sequence variants.

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Dissertations / Theses on the topic "Sequence Analysis, DNA – methods"

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Henderson, Daniel Adrian. "Modelling and analysis of non-coding DNA sequence data." Thesis, University of Newcastle Upon Tyne, 1999. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.299427.

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Chen, Zhuo. "Smart Sequence Similarity Search (S⁴) system." CSUSB ScholarWorks, 2004. https://scholarworks.lib.csusb.edu/etd-project/2458.

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Sequence similarity searching is commonly used to help clarify the biochemical and physiological features of newly discovered genes or proteins. An efficient similarity search relies on the choice of tools and their associated subprograms and numerous parameter settings. To assist researchers in selecting optimal programs and parameter settings for efficient sequence similarity searches, the web-based expert system, Smart Sequence Similarity Search (S4) was developed.

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Roth, Christian [Verfasser]. "Statistical methods for biological sequence analysis for DNA binding motifs and protein contacts / Christian Roth." Göttingen : Niedersächsische Staats- und Universitätsbibliothek Göttingen, 2021. http://nbn-resolving.de/urn:nbn:de:gbv:7-21.11130/00-1735-0000-0008-5912-0-2.

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Bajak, Edyta Zofia. "Genotoxic stress: novel biomarkers and detection methods : uncovering RNAs role in epigenetics of carcinogenesis /." Stockholm, 2005. http://diss.kib.ki.se/2005/91-7140-415-5/.

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Gelfond, Jonathan A. L. Ibrahim Joseph George. "Bayesian model-based methods for the analysis of DNA microarrays with survival, genetic, and sequence data." Chapel Hill, N.C. : University of North Carolina at Chapel Hill, 2007. http://dc.lib.unc.edu/u?/etd,972.

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Thesis (Ph. D.)--University of North Carolina at Chapel Hill, 2007.<br>Title from electronic title page (viewed Dec. 18, 2007). "... in partial fulfillment of the requirements for the degree of Doctor of Philosophy in the Department of Biostatistics, School of Public Health." Discipline: Biostatistics; Department/School: Public Health.

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Tan, Angela Y. C. "The development of an efficient method of mitochondrial DNA analysis." Monash University, Dept. of Forensic Medicine, 2003. http://arrow.monash.edu.au/hdl/1959.1/9525.

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Lu, Yang 1972. "High throughput study of the translational effect of human single nucleotide polymorphisms." Thesis, McGill University, 2008. http://digitool.Library.McGill.CA:80/R/?func=dbin-jump-full&object_id=116089.

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Introduction: As a part of the Gene Regulators in Disease project (GRID), this study aims to create a novel high throughput method to discover the genetic effect on gene translation, taking advantage of the rationale that efficiently translated mRNAs associate with multiple ribosomes, while less active ones with fewer or none.<br>Methods: Lymphoblastoid cell lines (LCLs) from 44 HapMap European individuals were used for polyribosomal fractionation and establishing the sample bank for the future study. The fractionated mRNA samples of 10 out of the 44 individuals were run on an Illumina GoldenGate Beadarray to detect allelic imbalance (developed by the group of T.J. Hudson and T.M. Pastinen).<br>Results: This study established a high-quality RNA bank, including 1,100 RNA fraction samples. By the Illumina chip, translational imbalance was detected in 75 out of 1483 (5.06%) assays, and 63 out of269 (23.4%) genes. The translational effect was well replicable by the resequencing method.<br>Conclusion: This study found that genetic effect on gene translation is a common mechanism of expression regulation. Our best hit found in the integrin beta 1 binding protein 1 gene (ITGB1BP1 ) highlights the role of mRNA 3'UTR secondary structure in gene translation.<br>Keywords: Gene translation, High throughput genotyping, Human genetics, Polyribosome, RNA, Single nucleotide polymorphism

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Morozov, Vyacheslav. "Computational Methods for Inferring Transcription Factor Binding Sites." Thèse, Université d'Ottawa / University of Ottawa, 2012. http://hdl.handle.net/10393/23382.

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Position weight matrices (PWMs) have become a tool of choice for the identification of transcription factor binding sites in DNA sequences. PWMs are compiled from experimentally verified and aligned binding sequences. PWMs are then used to computationally discover novel putative binding sites for a given protein. DNA-binding proteins often show degeneracy in their binding requirement, the overall binding specificity of many proteins is unknown and remains an active area of research. Although PWMs are more reliable predictors than consensus string matching, they generally result in a high number of false positive hits. A previous study introduced a novel method to PWM training based on the known motifs to sample additional putative binding sites from a proximal promoter area. The core idea was further developed, implemented and tested in this thesis with a large scale application. Improved mono- and dinucleotide PWMs were computed for Drosophila melanogaster. The Matthews correlation coefficient was used as an optimization criterion in the PWM refinement algorithm. New PWMs keep an account of non-uniform background nucleotide distributions on the promoters and consider a larger number of new binding sites during the refinement steps. The optimization included the PWM motif length, the position on the promoter, the threshold value and the binding site location. The obtained predictions were compared for mono- and dinucleotide PWM versions with initial matrices and with conventional tools. The optimized PWMs predicted new binding sites with better accuracy than conventional PWMs.

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Wessel, Jennifer. "Human genetic-epidemiologic association analysis via allelic composition and DNA sequence similarity methods applications to blood-based gene expression biomarkers of disease /." Connect to a 24 p. preview or request complete full text in PDF format. Access restricted to UC campuses, 2006. http://wwwlib.umi.com/cr/ucsd/fullcit?p3237548.

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Thesis (Ph. D.)--University of California, San Diego and San Diego State University, 2006.<br>Title from first page of PDF file (viewed December 12, 2006). Available via ProQuest Digital Dissertations. Vita. Includes bibliographical references.

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Paci, Giulia. "Statistical methods for the analysis of DNA sequences: application to dinucleotide distribution in the human genome." Master's thesis, Alma Mater Studiorum - Università di Bologna, 2014. http://amslaurea.unibo.it/7615/.

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Questa tesi si inserisce nell'ambito delle analisi statistiche e dei metodi stocastici applicati all'analisi delle sequenze di DNA. Nello specifico il nostro lavoro è incentrato sullo studio del dinucleotide CG (CpG) all'interno del genoma umano, che si trova raggruppato in zone specifiche denominate CpG islands. Queste sono legate alla metilazione del DNA, un processo che riveste un ruolo fondamentale nella regolazione genica. La prima parte dello studio è dedicata a una caratterizzazione globale del contenuto e della distribuzione dei 16 diversi dinucleotidi all'interno del genoma umano: in particolare viene studiata la distribuzione delle distanze tra occorrenze successive dello stesso dinucleotide lungo la sequenza. I risultati vengono confrontati con diversi modelli nulli: sequenze random generate con catene di Markov di ordine zero (basate sulle frequenze relative dei nucleotidi) e uno (basate sulle probabilità di transizione tra diversi nucleotidi) e la distribuzione geometrica per le distanze. Da questa analisi le proprietà caratteristiche del dinucleotide CpG emergono chiaramente, sia dal confronto con gli altri dinucleotidi che con i modelli random. A seguito di questa prima parte abbiamo scelto di concentrare le successive analisi in zone di interesse biologico, studiando l’abbondanza e la distribuzione di CpG al loro interno (CpG islands, promotori e Lamina Associated Domains). Nei primi due casi si osserva un forte arricchimento nel contenuto di CpG, e la distribuzione delle distanze è spostata verso valori inferiori, indicando che questo dinucleotide è clusterizzato. All’interno delle LADs si trovano mediamente meno CpG e questi presentano distanze maggiori. Infine abbiamo adottato una rappresentazione a random walk del DNA, costruita in base al posizionamento dei dinucleotidi: il walk ottenuto presenta caratteristiche drasticamente diverse all’interno e all’esterno di zone annotate come CpG island. Riteniamo pertanto che metodi basati su questo approccio potrebbero essere sfruttati per migliorare l’individuazione di queste aree di interesse nel genoma umano e di altri organismi.

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Books on the topic "Sequence Analysis, DNA – methods"

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Chemeris, A. V. Sekvenirovanie DNK. Nauka, 1999.

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Tiling arrays: Methods and protocols. Humana Press, 2013.

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Ancient DNA typing: Methods, strategies, and applications. Springer, 2003.

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Data analysis tools for DNA microarrays. Chapman & Hall/CRC, 2003.

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Kasprzak, Marta. Combinatorial models and methods for reading genomic sequences. Wydawn. Politechniki Poznańskiej, 2004.

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Kahl, Günter, and Matthias Harbers. Tag-based next generation sequencing. Wiley-Blackwell, 2012.

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Genetic variation: Methods and protocols. Humana Press, 2010.

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Zidong, Wang, and Liu Xiaohui, eds. Microarray image analysis: An algorithmic approach. Chapman & Hall/CRC, 2010.

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Mobile DNA: Finding treasure in junk. FT Press, 2011.

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Dongguang, Li, ed. DNA microarray technology and data analysis in cancer research. World Scientific, 2008.

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Book chapters on the topic "Sequence Analysis, DNA – methods"

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Rozas, Julio. "DNA Sequence Polymorphism Analysis Using DnaSP." In Methods in Molecular Biology. Humana Press, 2009. http://dx.doi.org/10.1007/978-1-59745-251-9_17.

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Ewens, Warren J., and Gregory R. Grant. "The Analysis of One DNA Sequence." In Statistical Methods in Bioinformatics. Springer New York, 2001. http://dx.doi.org/10.1007/978-1-4757-3247-4_5.

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Minton, Jayne A. L., Sarah E. Flanagan, and Sian Ellard. "Mutation Surveyor: Software for DNA Sequence Analysis." In Methods in Molecular Biology. Humana Press, 2010. http://dx.doi.org/10.1007/978-1-60761-947-5_10.

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Newkirk, Marianna, Katheryn Meek, Witold Cieplak, Charles Hasemann, and J. Donald Capra. "The Synergism of Protein Chemistry and Recombinant DNA Techniques." In Methods in Protein Sequence Analysis · 1986. Humana Press, 1987. http://dx.doi.org/10.1007/978-1-59259-480-1_4.

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Baxevanis, Andreas D. "Predictive Methods Using DNA Sequences." In Methods of Biochemical Analysis. John Wiley & Sons, Inc., 2002. http://dx.doi.org/10.1002/0471223921.ch10.

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Robey, Frank A. "The Evolution of the Regulatory Response to Products of Recombinant DNA Technology." In Methods in Protein Sequence Analysis · 1986. Humana Press, 1987. http://dx.doi.org/10.1007/978-1-59259-480-1_5.

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Victorino, Íris Marisa Maxaieie, Andrea Berruti, Alberto Orgiazzi, Samuele Voyron, Valeria Bianciotto, and Erica Lumini. "High-Throughput DNA Sequence-Based Analysis of AMF Communities." In Methods in Molecular Biology. Springer US, 2020. http://dx.doi.org/10.1007/978-1-0716-0603-2_9.

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Shattuck-Eidens, Donna M., Russell N. Bell, and Timothy Helentjaris. "Detection of DNA sequence variation for genome analysis." In Plant Genomes: Methods for Genetic and Physical Mapping. Springer Netherlands, 1992. http://dx.doi.org/10.1007/978-94-011-2442-3_4.

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Kans, Jonathan A., and B. F. Francis Ouellette. "Submitting DNA Sequences to the Databases." In Methods of Biochemical Analysis. John Wiley & Sons, Inc., 2006. http://dx.doi.org/10.1002/9780470110607.ch14.

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Kans, Jonathan A., and B. F. Francis Ouellette. "Submitting DNA Sequences to the Databases." In Methods of Biochemical Analysis. John Wiley & Sons, Inc., 2002. http://dx.doi.org/10.1002/0471223921.ch4.

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Conference papers on the topic "Sequence Analysis, DNA – methods"

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"APPLYING CONCEPTUAL MODELING TO ALIGNMENT TOOLS ONE STEP TOWARDS THE AUTOMATION OF DNA SEQUENCE ANALYSIS." In International Conference on Bioinformatics Models, Methods and Algorithms. SciTePress - Science and and Technology Publications, 2011. http://dx.doi.org/10.5220/0003142001370142.

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Oueslati, Afef Elloumi, Zied Lachiri, and Noureddine Ellouze. "Spectral Analysis of DNA Sequence: The Exon's Location Method." In 2007 15th International Conference on Digital Signal Processing. IEEE, 2007. http://dx.doi.org/10.1109/icdsp.2007.4288532.

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Roy, M., and S. Barman Mandal. "Spectral analysis of coding and non-coding regions of a DNA sequence by Parametric method." In 2010 Annual IEEE India Conference (INDICON). IEEE, 2010. http://dx.doi.org/10.1109/indcon.2010.5712676.

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Kaida, S., T. Miyata, S. Kawabata, et al. "NUCLEOTIDE SEQUENCE OF THE STAPHYLOCOAGULASE GENE FROM STAPHYLOCOCCUS AUREUS STRAIN BB." In XIth International Congress on Thrombosis and Haemostasis. Schattauer GmbH, 1987. http://dx.doi.org/10.1055/s-0038-1644607.

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Staphylocoagulase (SC) is a secretary protein produced by several strains of Staphylococcus aureus (S. aureus). This protein forms a molecular complex ("staphylothrombin") with human prothrombin in a molar ratio of 1:1. The complex displays the ability to clot fibrinogen and to hydrolyze the synthetic tripeptide substrates for α-thrombin. The formation of staphylothrombin does not require proteolytic cleavage of the prothrombin molecule, and this mechanism differs markedly from the activation process by either blood-clotting factor Xa or snake venom procoagulant.In the present studies, a pAT153 library containing partial Mbo I-digested DNA prepared from aureus strain BB has been screened with a fibrin gel formation method. The identity of these clones with SC was confirmed by DNA sequence analysis and by comparison of the derived amino acid sequence with that determined for the purified SC protein. One of the positive colonies was isolated and 3.1 Kb of the insert DNA was determined by the dideoxy chain termination method. The results indicated that the insert DNA consists of 148 bp 5' flanking region, protein coding region of 715 amino acids and 746 bp 3' flanking region, and that SC from strain BB is synthesized as a precursor with a signal peptide of 26 amino acids. Thus, the mature form was composed of 689 amino acids with a molecular weight of 77,337- The NH2-terminal sequence (324 amino acids) of SC isolated from S. aureus strain 213 (S. Kawabata et al. (1986): J. Biol. Chem. 261, 527-531) was compared with that of SC derived from strain BB. The sequence homology between them was found to show 57 %. It was also found that SC derived from strain BB was composed of 8 tandem repeats (27 amino acid residues in length) in the COOH-terminal region, although their functions are not known.

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Belyakova, N. V., E. A. Vorobyova, and V. A. Sivolapov. "MOLECULAR-GENETIC ANALYSIS OF PHYTOPATHOGENS IN STANDS OF THE VORONEZH REGION." In Modern machines, equipment and IT solutions for industrial complex: theory and practice. Voronezh State University of Forestry and Technologies named after G.F. Morozov, Voronezh, Russia, 2021. http://dx.doi.org/10.34220/mmeitsic2021_29-33.

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This paper presents the results of DNA diagnostics of phytopathogens in the Voronezh region. DNA diagnostics was carried out step by step: isolation of total DNA from the sample by CTAB method, amplification of marker regions of phytopathogenic organisms using primers ITS1 and ITS4, electrophoretic separation of the obtained amplicons in 2% agarose gel followed by staining with ethidium bromide, determination of the nucleotide sequence of the amplified loci ABI Prism 310. The study identified the following plant diseases: Sphaeropsis sapinea, Rhizoctonia solani, Cladosporium herbarum. Along with this, we identified the Neocatenulostroma pathogen, which had not previously been found in the territories under its jurisdiction. This disease cannot be determined by phenological signs. The degree of infection by pathogens ranged from 15 to 40%. At present, the problem of protecting plants from diseases is especially urgent. It has been established that the greatest damage to forestry activities is caused by fungal and infectious diseases. At the same time, among phytopathogens, about 97% are fungal infections, 2% are bacterial and 1% are viral.

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Santhosh Kumar, G., and S. H. Shiji. "DNA sequence representation methods." In the International Symposium. ACM Press, 2010. http://dx.doi.org/10.1145/1722024.1722073.

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Yeh, Hsin-Chih, Christopher M. Puleo, Yi-Ping Ho, and Tza-Huei Wang. "Towards Single-Molecule Diagnostics Using Microfluidic Manipulation and Quantum Dot Nanosensors." In ASME 2007 5th International Conference on Nanochannels, Microchannels, and Minichannels. ASMEDC, 2007. http://dx.doi.org/10.1115/icnmm2007-30213.

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In this report, we review several single-molecule detection (SMD) methods and newly developed nanocrystal-mediated single-fluorophore strategies for ultrasensitive and specific analysis of genomic sequences. These include techniques, such as quantum dot (QD)-mediated fluorescence resonance energy transfer (FRET) technology and dual-color fluorescence coincidence and colocalization analysis, which allow separation-free detection of low-abundance DNA sequences and mutational analysis of oncogenes. Microfluidic approaches developed for use with single-molecule detection to achieve rapid, low-volume, and quantitative analysis of nucleic acids, such as electrokinetic manipulation of single molecules and confinement of sub-nanoliter samples using microfluidic networks integrated with valves, are also discussed.

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Kumar, Anoop, Inderjit Singh Yadav, Rupinder Sekhon, Dwaipayan Bharadwaj, and Mausumi Bharadwaj. "Identification of T- and B-cell epitopes in HPV-16 E7 gene isolated from cervical cancer patients." In 16th Annual International Conference RGCON. Thieme Medical and Scientific Publishers Private Ltd., 2016. http://dx.doi.org/10.1055/s-0039-1685256.

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Abstract:

Introduction: In India, cervical cancer is the most common cancer among females. Persistence infection with high risk human papillomaviruses (HR-HPV) is an etiological agent for cervical cancer development, especially HPV-16 is found to be exclusively high in cervical cancer cases in Indian population. The continuous expression and transforming ability of HPV E7 helps in progression of cervical cancer and other HPV related disease, which make E7 as a suitable targets for the development of therapeutic vaccines. Objectives: Identification of T-& B-cell epitopes HPV-16 E7 gene isolated from in cervical cancer patients. Materials and Methods: A total of 80 cervical cancer tissue biopsies were collected and processed for DNA extraction, HPV diagnosis and genotyping. E7 gene of HPV-16 positive samples were amplified and sequenced. Epitopes in E7 gene sequence were predicted by online freely available tools. Results: In the present study we got 72 samples (90%) were positive for HPV and out of which 68 samples (94.4%) were positive for the HPV-16. HPV-16 positive samples were sequenced and translated. IEDB server was used for epitope analysis; 12 potent epitopes for the MHC-I alleles were identified in isolated E7 gene of HPV-16. The most potent epitopes were MHGDTPTLHEYM for HLA-C*07:01; LLMGTLGIVCPI for HLA-A*02:01 and MHGDTPTLHEYML for HLA-C*07:01; having percentile rank 0.2 for all three and antigencity score of 0.20011, 0.15358 and 0.10735, respectively. Conclusion: This is an effective strategy to design immuno-therapeutics and therapeutic vaccine against HPV using E7 as target. These findings will be helpful in the development of effective vaccine for particular geographical region.

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Nacong, Nasria, Desy Lusiyanti, and Muhammad Isa Irawan. "Sequence analysis of Leukemia DNA." In SYMPOSIUM ON BIOMATHEMATICS (SYMOMATH) 2017. Author(s), 2018. http://dx.doi.org/10.1063/1.5026082.

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Brennan, Thomas, John Chakel, P. Bente, and Mark Field. "New methods to sequence DNA by mass spectrometry." In OE/LASE '90, 14-19 Jan., Los Angeles, CA, edited by Gary C. Salzman. SPIE, 1990. http://dx.doi.org/10.1117/12.17813.

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Reports on the topic "Sequence Analysis, DNA – methods"

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Shavlik, J. W. Applying machine learning techniques to DNA sequence analysis. Office of Scientific and Technical Information (OSTI), 1992. http://dx.doi.org/10.2172/5688406.

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Shavlik, J. W., and M. O. Noordewier. Applying machine learning techniques to DNA sequence analysis. Office of Scientific and Technical Information (OSTI), 1992. http://dx.doi.org/10.2172/7023074.

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Uberbacher, E. C., Y. Xu, M. B. Shah, V. Olman, M. Parang, and R. Mural. An editing environment for DNA sequence analysis and annotation. Office of Scientific and Technical Information (OSTI), 1998. http://dx.doi.org/10.2172/563243.

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Shavlik, J. W., and M. O. Noordewier. Applying machine learning techniques to DNA sequence analysis. Final report. Office of Scientific and Technical Information (OSTI), 1995. http://dx.doi.org/10.2172/564145.

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Walt, D. R., and K.-H. Lee. Time-Resolved Sequence Analysis on High Density Fiberoptic DNA Probe. Office of Scientific and Technical Information (OSTI), 2002. http://dx.doi.org/10.2172/834517.

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Wallace, Susan S. Structure/Function Analysis of DNA-glycosylases That Repair Oxidized Purines and Pyrimidines and the Influence of Surrounding DNA Sequence on Their Interactions. Office of Scientific and Technical Information (OSTI), 2005. http://dx.doi.org/10.2172/900301.

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Manning, Ruth Ann. GRAIL-genQuest: A comprehensive computational system for DNA sequence analysis. Final report, DOE SBIR Phase II. Office of Scientific and Technical Information (OSTI), 1999. http://dx.doi.org/10.2172/770188.

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Shavlik, J. W. Applying machine learning techniques to DNA sequence analysis. Progress report, February 14, 1991--February 13, 1992. Office of Scientific and Technical Information (OSTI), 1992. http://dx.doi.org/10.2172/10135095.

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Wu, Liyou, T. Y. Yi, Joy Van Nostrand, and Jizhong Zhou. Phylogenetic Analysis of Shewanella Strains by DNA Relatedness Derived from Whole Genome Microarray DNA-DNA Hybridization and Comparison with Other Methods. Office of Scientific and Technical Information (OSTI), 2010. http://dx.doi.org/10.2172/986917.

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Shavlik, J. W., and M. O. Noordewier. Applying machine learning techniques to DNA sequence analysis. Progress report, Year 2, February 14, 1992--December 11, 1992. Office of Scientific and Technical Information (OSTI), 1992. http://dx.doi.org/10.2172/10124406.

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