Rozprawy doktorskie na temat „DNA sequencing”
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Chen, Ying-Ja. "DNA sequencing by denaturation". Diss., [La Jolla] : University of California, San Diego, 2009. http://wwwlib.umi.com/cr/ucsd/fullcit?p3359122.
Pełny tekst źródłaTitle from first page of PDF file (viewed July 14, 2009). Available via ProQuest Digital Dissertations. Vita. Includes bibliographical references (p. 87-91).
Leah, Labib. "Helicase Purification for DNA Sequencing". Thesis, Université d'Ottawa / University of Ottawa, 2014. http://hdl.handle.net/10393/31341.
Pełny tekst źródłaBoufounos, Petros T. 1977. "Signal processing for DNA sequencing". Thesis, Massachusetts Institute of Technology, 2002. http://hdl.handle.net/1721.1/17536.
Pełny tekst źródłaIncludes bibliographical references (p. 83-86).
DNA sequencing is the process of determining the sequence of chemical bases in a particular DNA molecule-nature's blueprint of how life works. The advancement of biological science in has created a vast demand for sequencing methods, which needs to be addressed by automated equipment. This thesis tries to address one part of that process, known as base calling: it is the conversion of the electrical signal-the electropherogram--collected by the sequencing equipment to a sequence of letters drawn from ( A,TC,G ) that corresponds to the sequence in the molecule sequenced. This work formulates the problem as a pattern recognition problem, and observes its striking resemblance to the speech recognition problem. We, therefore, propose combining Hidden Markov Models and Artificial Neural Networks to solve it. In the formulation we derive an algorithm for training both models together. Furthermore, we devise a method to create very accurate training data, requiring minimal hand-labeling. We compare our method with the de facto standard, PHRED, and produce comparable results. Finally, we propose alternative HMM topologies that have the potential to significantly improve the performance of the method.
by Petros T. Boufounos.
M.Eng.and S.B.
Blomstergren, Anna. "Strategies for de novo DNA sequencing". Doctoral thesis, KTH, Biotechnology, 2003. http://urn.kb.se/resolve?urn=urn:nbn:se:kth:diva-3649.
Pełny tekst źródłaThe development of improved sequencing technologies hasenabled the field of genomics to evolve. Handling andsequencing of large numbers of samples require an increasedlevel of automation in order to obtain high throughput andconsistent quality. Improved performance has lead to thesequencing of numerous microbial genomes and a few genomes fromhigher eukaryotes and the benefits of comparing sequences bothwithin and between species are now becoming apparent. Thisthesis describes both the development of automated purificationmethods for DNA, mainly sequencing products, and a comparativesequencing project.
The initially developed purification technique is dedicatedto single stranded DNA containing vector specific sequences,exemplified by sequencing products. Specific capture probescoupled to paramagnetic beads together with stabilizing modularprobes hybridize to the single stranded target. After washing,the purified DNA can be released using water. When sequencingproducts are purified they can be directly loaded onto acapillary sequencer after elution. Since this approach isspecific it can be applied to multiplex sequencing products.Different probe sets are used for each sequencing product andthe purifications are performed iteratively.
The second purification approach, which can be applied to anumber of different targets, involves biotinylated PCR productsor sequencing products that are captured using streptavidinbeads. This has been described previously, buthere theinteraction between streptavidin and biotin can be disruptedwithout denaturing the streptavidin, enabling the re-use of thebeads. The relatively mild elution conditions also enable therelease of sensitive biotinylated molecules.
Another project described in this thesis is the comparativesequencing of the 40 kbcagpathogenicity island (PAI) in fourHelicobacter pyloristrains. The results included thediscovery of a novel gene, present in approximately half of theSwedish strains tested. In addition, one of the strainscontained a major rearrangement dividing thecagPAI into two parts. Further, information about thevariability of different genes could be obtained.
Keywords:DNA sequencing, DNA purification, automation,solid-phase, streptavidin, biotin, modular probes,Helicobacter pylori,cagPAI.
Hu, Yue. "Microbial DNA Sequencing in Environmental Studies". Doctoral thesis, KTH, Skolan för bioteknologi (BIO), 2017. http://urn.kb.se/resolve?urn=urn:nbn:se:kth:diva-204897.
Pełny tekst źródłaYue Hu was supported by a scholarship from the China Scholarship Council (CSC #201206950024)
Yue Hu has been publishing papers under the name "Yue O. O. Hu".
QC 20170403
Peng, Hongbo. "Towards hybridization-assisted nanopore DNA sequencing". View abstract/electronic edition; access limited to Brown University users, 2008. http://gateway.proquest.com/openurl?url_ver=Z39.88-2004&rft_val_fmt=info:ofi/fmt:kev:mtx:dissertation&res_dat=xri:pqdiss&rft_dat=xri:pqdiss:3318349.
Pełny tekst źródłaHaan, Nicholas. "Statistical models and algorithms for DNA sequencing". Thesis, University of Cambridge, 2001. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.396070.
Pełny tekst źródłaDezfouli, Mahya. "Barcoded DNA Sequencing for Parallel Protein Detection". Doctoral thesis, KTH, Genteknologi, 2015. http://urn.kb.se/resolve?urn=urn:nbn:se:kth:diva-159506.
Pełny tekst źródłaQC 20150203
Hu, Yuwei S. M. Massachusetts Institute of Technology, i Chin Soon Lim. "Scheduling of biological samples for DNA sequencing". Thesis, Massachusetts Institute of Technology, 2009. http://hdl.handle.net/1721.1/54214.
Pełny tekst źródłaThis electronic version was submitted by the student author. The certified thesis is available in the Institute Archives and Special Collections.
Cataloged from student submitted PDF version of thesis.
Includes bibliographical references (p. 95-97).
In a DNA sequencing workflow, a biological sample has to pass through multiple process steps. Two consecutive steps are hydroshearing and library construction. Samples arrive randomly into the inventory and are to complete both processes before their due dates. The research project is to decide the optimal sequence of samples to go through these two processes subject to operational constraints. Two approaches, namely, heuristic and integer programming have been pursued in this thesis. A heuristic algorithm is proposed to solve the scheduling problem. A variant of the problem involving deterministic arrivals of samples is also considered for comparison purposes. Comparison tests between the two approaches are carried out to investigate the performance of the proposed heuristic for the original problem and its variant. Sensitivity analysis of the schedule to parameters of the problem is also conducted when using both approaches.
by Yuwei Hu and Chin Soon Lim.
S.M.
Santiago, Garcia Eric, i Aspåker Hannes Salomonsson. "Temporal Convolutional Networks for Nanopore DNA Sequencing". Thesis, KTH, Skolan för elektroteknik och datavetenskap (EECS), 2020. http://urn.kb.se/resolve?urn=urn:nbn:se:kth:diva-295625.
Pełny tekst źródłaEn nyligen utvecklad metod för att sekvensera DNA innefattar att en elektrisk signal moduleras genom att nukleotider passerar genom porer i nanostorlek. I kommersiella lösningar analyseras denna signal med hjälp av maskininlärning via Recurrent Neural Networks, men en variant av neruala nätverk som kallas Temporal Convolution Networks har nyligen har visat sig ha bättre prestanda jämfört med Recurrent Networks för olika typer av signalbehandlingsproblem. Målet med detta projekt är att undersöka användbarheten av Temporal Convolutional Networks för en förenklad version av DNA-sekvensering, där uppdraget endast är att identifera de nukleotider som passerar genom poren vid varje given tidpunkt, istället för att rekonstruera en komplett DNA-sekvens. För att kunna bestämma en optimal arkitektur på nätverket så undersöks effekten av flera olika parametrar. De implementerade nätverken visas ha god förmåga att klassificera nukleotider, men är troligtvis i behov av ytterligare förbättringar för att kunna konkurrera med nuvarande kommersiella lösningar.
Kandidatexjobb i elektroteknik 2020, KTH, Stockholm
Arner, Erik. "Solving repeat problems in shotgun sequencing /". Stockholm, 2006. http://diss.kib.ki.se/2006/91-7140-996-3/.
Pełny tekst źródłaDavies, Stephen William. "Application of communication theory to automatic DNA sequencing". Thesis, National Library of Canada = Bibliothèque nationale du Canada, 1999. http://www.collectionscanada.ca/obj/s4/f2/dsk1/tape8/PQDD_0005/NQ41137.pdf.
Pełny tekst źródłaLundin, Sverker. "Methods to Prepare DNA for Efficient Massive Sequencing". Doctoral thesis, KTH, Genteknologi, 2012. http://urn.kb.se/resolve?urn=urn:nbn:se:kth:diva-105116.
Pełny tekst źródłaQC 20121126
Liang, Lijun. "Computational studies of DNA sequencing with graphene nanopores". Doctoral thesis, KTH, Teoretisk kemi och biologi, 2014. http://urn.kb.se/resolve?urn=urn:nbn:se:kth:diva-157664.
Pełny tekst źródłaQC 20141212
Arram, James. "FPGA acceleration of DNA sequencing analysis and storage". Thesis, Imperial College London, 2017. http://hdl.handle.net/10044/1/56867.
Pełny tekst źródłaQuick, Joshua. "Real-time pathogen surveillance systems using DNA sequencing". Thesis, University of Birmingham, 2018. http://etheses.bham.ac.uk//id/eprint/8135/.
Pełny tekst źródłaElmouelhi, Ahmed (Ahmed M. ). 1979. "Genome scanning : an AFM-based DNA sequencing technique". Thesis, Massachusetts Institute of Technology, 2003. http://hdl.handle.net/1721.1/34149.
Pełny tekst źródłaIncludes bibliographical references (p. 157-160).
Genome Scanning is a powerful new technique for DNA sequencing. The method presented in this thesis uses an atomic force microscope with a functionalized cantilever tip to sequence single stranded DNA immobilized to a mica surface. The functionalized cantilever tip hybridizes with only one base type (A, C, T, or G) and results in distinct peaks in the AFM-produced image. Genome Scanning has been successful at identifying 40 base strands of synthesized DNA and has been shown to detect a particular base type on 48 kilobase strands of lambda DNA. Currently, Genome Scanning is only accurate to 3-26 bases at a time, however, it can achieve a sequencing speed of 6000 bases/sec. In other words, Genome Scanning can be used to sequence the 3 billion bases of the human genome in 5.78 days.
by Ahmed Elmouelhi.
S.M.
Schwartz, Jerrod Joseph. "Technologies for high throughput single molecule DNA sequencing /". May be available electronically:, 2009. http://proquest.umi.com/login?COPT=REJTPTU1MTUmSU5UPTAmVkVSPTI=&clientId=12498.
Pełny tekst źródłaSharma, Prashant. "Hardware accelerator for SOM based DNA sequencing Algorithm". Thesis, KTH, Skolan för elektroteknik och datavetenskap (EECS), 2018. http://urn.kb.se/resolve?urn=urn:nbn:se:kth:diva-251808.
Pełny tekst źródłaClark, Graeme T. "A study of DNA repair". Thesis, University of Southampton, 1999. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.302000.
Pełny tekst źródłaMitra, Robi David. "Polony sequencing : DNA sequencing technology and a computational analysis reveals chromosomal domains of gene expression". Thesis, Massachusetts Institute of Technology, 2000. http://hdl.handle.net/1721.1/8797.
Pełny tekst źródłaIncludes bibliographical references.
The first part of this thesis describes the development of polony sequencing, a sequencing technology in which DNA is cloned, amplified and sequenced in a polymer matrix. A complex library of one to ten million linear DNA molecules is amplified by performing polymerase chain reaction (PCR) in a thin polyacrylamide film poured on a glass microscope slide. The polyacrylamide matrix retards the diffusion of the DNA molecules so that each amplification product remains localized near its parent molecule. At the end of the reaction, a number of polymerase colonies, or "polonies", have formed, each one grown from a single template molecule. As many as 5 million clones can be amplified in parallel on a single slide. By including an acrydite modification at the 5' end of one of the PCR primers, the amplified DNA will be covalently attached to the polyacrylamide matrix, allowing further enzymatic manipulations to be performed on all clones simultaneously. Also described in this thesis is my progress in development of a protocol to sequence the polonies by repeated cycles of extension with fluorescent deoxynucleotide. Because polony sequencing is inherently parallel, and sub-picoliter volumes are used for each reaction, the technology should be substantially faster and cheaper than existing methods. Applications for polony sequencing such as gene expression analysis, SNP discovery, and SNP screening will also be discussed. The second part of this thesis describes a computational analysis that tests the hypothesis that chromosomal position affects gene expression. It is shown that, throughout the genome, genes lying close together on the same chromosome often show significant coexpression. This coexpression is independent of the orientation of genes to each other, but is dependent on the distance between genes. In several cases where adjacent genes show highly correlated expression, the promoter of only one of the genes contains an upstream activating sequence (UAS) known to be associated with the expression pattern. These results suggest that in certain regions of the genome a single transcription factor binding site may regulate several genes. It is also shown that evolution may take advantage of this phenomenon by keeping genes with similar functions in adjacent positions along the chromosomes. The techniques that are presented provide a computational method to delineate the locations of chromosomal domains and identify the boundary elements that flank them.
Robi David Mitra.
Ph.D.
Voss, Karl O. "Capillary electrophoresis for DNA sequencing and cytosine methylation analysis". Thesis, National Library of Canada = Bibliothèque nationale du Canada, 1998. http://www.collectionscanada.ca/obj/s4/f2/dsk2/ftp02/NQ29120.pdf.
Pełny tekst źródłaFERNANDES, ERALDO LUIS REZENDE. "HEURISTICS FOR THE PROBLEM OF DNA SEQUENCING BY HYBRIDIZATION". PONTIFÍCIA UNIVERSIDADE CATÓLICA DO RIO DE JANEIRO, 2005. http://www.maxwell.vrac.puc-rio.br/Busca_etds.php?strSecao=resultado&nrSeq=6412@1.
Pełny tekst źródłaO seqüenciamento por hibridação é uma alternativa interessante para a tarefa de seqüenciamento de DNA. Este método ainda está sendo aperfeiçoado e pode superar as técnicas utilizadas em termos de tempo e custo. Uma etapa crucial do método consiste em resolver um problema combinatório que pode ser formulado como um caso especial do problema do caixeiro viajante com coleta de prêmios. Neste trabalho, propõe-se uma nova heurística construtiva multi-partida para resolver este problema. Uma estratégia de aprendizado baseada em uma memória adaptativa e um procedimento de construção de vocabulário são utilizados para melhorar o desempenho da heurística multi-partida. A memória adaptativa é utilizada para intensificar as construções de novas soluções com os elementos que aparecem com uma freqüência maior nas melhores soluções encontradas anteriormente pela heurística multi-partida. O procedimento de construção de vocabulário consiste em construir novas soluções através da combinação de partes comuns a boas soluções. Testes computacionais mostraram que estas duas estratégias aumentam significativamente o desempenho da heurística multi-partida e são particularmente indicadas para problemas de escalonamento nos quais as melhores soluções são na maioria dos casos formadas por blocos de elementos que aparecem juntos com muita freqüência. A heurística proposta supera os resultados dos melhores algoritmos encontrados na literatura, tanto em termos da qualidade das soluções encontradas, como do tempo de computação.
Sequencing by hybridization is an attractive alternative for DNA sequencing. This novel method can be less time and cost consuming than the techniques applied nowadays. A very important step of this method is to solve a combinatorial problem formulated as a special case of the prize-collecting traveling salesman problem. In this work, we propose a new multistart construtive heuristic to solve this problem. A learning strategy based on adaptive memory and a vocabulary building procedure are used to improve the performance of the multistart heuristic. The adaptive memory is used to intensify the construction of new solutions with the elements that appear frequently in the best solutions previously found by the multistart heuristic. The objective of the vocabulary building procedure is to construct new solutions combining parts of good solutions. Computational experiments have shown that these two methods significantly improves the performance of the multistart heuristic and are particularly suitable for scheduling problems whose best solutions are in most cases built by blocks of elements that appear together very often. The proposed heuristic obtains systematically better solutions and is less time consuming than the best algorithms found in the literature.
Herena, Louis E. (Louis Eduardo) 1963. "Application of manufacturing tools in the DNA sequencing process". Thesis, Massachusetts Institute of Technology, 1999. http://hdl.handle.net/1721.1/80760.
Pełny tekst źródłaIncludes bibliographical references.
by Louis E. Herena.
S.M.
M.B.A.
Fritz, Markus Hsi-Yang. "Exploiting high throughput DNA sequencing data for genomic analysis". Thesis, University of Cambridge, 2012. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.610819.
Pełny tekst źródłaStoddart, David. "Progress towards ultra-rapid DNA sequencing with protein nanopores". Thesis, University of Oxford, 2011. http://ora.ox.ac.uk/objects/uuid:597b217c-c995-401d-b772-4cb373d195af.
Pełny tekst źródłaXu, D. Q. "Automatic interpretation of MWPC images of DNA sequencing gels". Thesis, University of Manchester, 1988. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.712123.
Pełny tekst źródłaStymne, Jakob, i Odeback Oliver Welin. "Evaluation of Temporal Convolutional Networks for Nanopore DNA Sequencing". Thesis, KTH, Skolan för elektroteknik och datavetenskap (EECS), 2020. http://urn.kb.se/resolve?urn=urn:nbn:se:kth:diva-295624.
Pełny tekst źródłaNanopore sequencing är en nyligen utvecklad metod för DNA-sekvensering som innebär att man applicerar ett konstant elektriskt fält över ett membran och translokerar enkelsträngade DNA-molekyler genom membranporer. Detta resulterar i en elektrisk signal som beror på DNA-strukturen. Målet med detta projekt är att träna och evaluera icke-kausula ”temporal convolutional networks” som ska kunna översätta denna ofiltrerade elektriska signalen till den motsvarande nukleotidsekvensen. Träningsdatan är ett urval av genomen från bakterien E. coli och viruset phage Lambda. Vi implementerade och utvärderade ett antal olika nätverksstrukturer. Ett nätverk med fem residuala block med fem faltande lager i varje block gav maximal prestation, med en precision på 76.1% på testdata. Detta resultat indikerar att ett ”temporal convolution network” skulle kunna vara ett effektivt sätt att sekvensera DNA.
Kandidatexjobb i elektroteknik 2020, KTH, Stockholm
Dutson, Claire L. "C5-modified 2'-deoxyuridine-5'-triphosphates for DNA sequencing". Thesis, University of Sheffield, 2015. http://etheses.whiterose.ac.uk/9172/.
Pełny tekst źródłaAllen, Esther. "C5-modified 2'-deoxycytidine-5'-triphosphates for DNA sequencing". Thesis, University of Sheffield, 2016. http://etheses.whiterose.ac.uk/12135/.
Pełny tekst źródłaKoh, Kyung Duk. "Repair, consequence, and profile of ribonucleotides in DNA". Diss., Georgia Institute of Technology, 2015. http://hdl.handle.net/1853/53534.
Pełny tekst źródłaSmith, Victoria. "A molecular genetic analysis of yeast chromosome IX". Thesis, University of Cambridge, 1992. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.239206.
Pełny tekst źródłaHawkins, Trevor. "Genome sequencing and analysis of 260Kb covering chromosome III of Caenorhabditis elegans". Thesis, University of Sussex, 1993. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.332544.
Pełny tekst źródłaAdams, Maria. "Genetic and functional analysis of the human thyroid hormones receptor beta". Thesis, University of Hertfordshire, 1998. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.262796.
Pełny tekst źródłaBowler, Frank Ray. "Reading DNA with PNA : a dynamic chemical approach to DNA sequence analysis". Thesis, University of Edinburgh, 2011. http://hdl.handle.net/1842/5270.
Pełny tekst źródłaBauer, David L. V. "Preparing and sequencing ultra-long DNA molecules from single chromosomes". Thesis, University of Oxford, 2013. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.640151.
Pełny tekst źródłaGraham, Joseph (Joseph Arthur). "An analysis of the next generation DNA sequencing technology market". Thesis, Massachusetts Institute of Technology, 2007. http://hdl.handle.net/1721.1/42360.
Pełny tekst źródłaIncludes bibliographical references (p. 57-60).
While there is no shortage of successful and failed biotechnology ventures, it is still very difficult to gage, a priori, how a new company will fare in this industry. In many cases new biotechnology ventures are driven by rapidly evolving technology and emergent customer needs, both unpredictable by nature. Also, the Biotech Industry faces increased public and federal scrutiny as companies attempt to navigate murky ethical and legal waters. This thesis will explore the ongoing development of the next generation DNA sequencing market in an effort to predict exactly which factors will play a role in determining who will ultimately succeed. This will be accomplished through an analysis incorporating a combination of historical precedents in this industry and traditional market theories. The goal is to produce a set of dimensions along which to judge the current and future participants in this market in order to determine which are most likely to succeed.
by Joseph Graham.
S.M.
Hogstrom, Larson J. "Return on investment and library complexity analysis for DNA sequencing". Thesis, Massachusetts Institute of Technology, 2016. http://hdl.handle.net/1721.1/104556.
Pełny tekst źródłaCataloged from PDF version of thesis.
Includes bibliographical references (page 49).
Understanding the profiles of information acquisition during DNA sequencing experiments is critical to the design and implementation of large-scale studies in medical and population genetics. One known technical challenge and cost driver in next-generation sequencing data is the occurrence of non-independent observations that are created from sequencing artifacts and duplication events from polymerase chain reaction (PCR). The current study demonstrates improved return on investment (ROI) modeling strategies to better anticipate the impact of non-independent observations in multiple forms of next-generation sequencing data. Here, a physical modeling approach based on Pó1ya urn was evaluated using both multi-point estimation and duplicate set occupancy vectors. The results of this study can be used to reduce sequencing costs by improving aspects of experimental design including sample pooling strategies, top-up events, and termination of non-informative samples.
by Larson J. Hogstrom.
S.M.
Song, Jamie 1977. "Optimization of data acquisition system for novel DNA sequencing instrument". Thesis, Massachusetts Institute of Technology, 2000. http://hdl.handle.net/1721.1/86500.
Pełny tekst źródłaIncludes bibliographical references (leaf 61).
by Jamie Song.
S.B.and M.Eng.
Kumar, Mayank S. M. Massachusetts Institute of Technology. "Development of a microfluidic platform for integrated DNA sequencing protocols". Thesis, Massachusetts Institute of Technology, 2007. http://hdl.handle.net/1721.1/40371.
Pełny tekst źródłaIncludes bibliographical references.
This thesis describes the design and development of a microfluidic platform to reduce costs and improve the quality of in the DNA sequencing methodology currently implemented at the Broad Institute in Cambridge, Massachusetts. The Sequencing Center at the Broad Institute currently generates an average of 130 million bases per day with an average read length of 800. This is enabled by the successful preparation and detection of over 97,000 unique samples. Most of the cost per sample is tied up in expensive proprietary reagents utilized in the various reactions comprising the preparation process. Through the application of microfluidics, the possibility of drastically scaling down the amount of proprietary reagents is explored. Stamp-sized elastomeric polydimethylsiloxane (PDMS) microfluidic devices were developed and microfluidic sample manipulation techniques were standardized. Using these devices and techniques, an attempt was made to adapt the various components of the sequencing process to the microfluidic platform. Work within the scope of this thesis is focused on the adaptation of the commercial sequencing protocols, which are labor intensive, consume costly reagents and serve as limitations for high-throughput parallelization of the process.
(cont.) The first is the amplification reaction. By scaling down the process from a plate-based format to an integrated microfluidic device, amplification reagent consumption was reduced by two orders of magnitude while maintaining the quality and length of the sequencing reads (with the subsequent sequencing reaction run off chip). As a follow up project, an attempt was made to scale down the Sequencing Reaction, which, in spite of limitations, suggested a good path toward the eventual development of an integrated microfluidic device for the preparation of running the complete sequencing reaction protocol on-chip.
by Mayank Kumar.
S.M.
Sigurgeirsson, Benjamín. "Analysis of RNA and DNA sequencing data : Improved bioinformatics applications". Doctoral thesis, KTH, Genteknologi, 2016. http://urn.kb.se/resolve?urn=urn:nbn:se:kth:diva-184158.
Pełny tekst źródłaQC 20160329
Camerlengo, Terry Luke. "Techniques for Storing and Processing Next-Generation DNA Sequencing Data". The Ohio State University, 2014. http://rave.ohiolink.edu/etdc/view?acc_num=osu1388502159.
Pełny tekst źródłaManara, Richard. "Free energy calculations of DNA translocation through protein nanopores and nanopore design for DNA sequencing". Thesis, University of Southampton, 2015. https://eprints.soton.ac.uk/374791/.
Pełny tekst źródłaBuschmann, Tilo. "The Systematic Design and Application of Robust DNA Barcodes". Doctoral thesis, Universitätsbibliothek Leipzig, 2016. http://nbn-resolving.de/urn:nbn:de:bsz:15-qucosa-209812.
Pełny tekst źródłaVan, der Vaart Maniesh. "Characterization of circulating free DNA in healthy and diseased individuals / Maniesh van der Vaart". Thesis, North-West University, 2009. http://hdl.handle.net/10394/5074.
Pełny tekst źródłaThornley, David John. "Analysis of trace data from fluorescence based Sanger sequencing". Thesis, Imperial College London, 1997. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.286265.
Pełny tekst źródłaBourin, Stephanie. "Novel strategies for DNA detection assay". Thesis, University of London, 1998. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.265939.
Pełny tekst źródłaRose, B. A. (Beverley Ann). "The characterisation and partial sequencing of the grapevine chloroplast genome". Thesis, Stellenbosch : Stellenbosch University, 2004. http://hdl.handle.net/10019.1/53763.
Pełny tekst źródłaENGLISH ABSTRACT: A number of proteins essential for the survival of a plant are encoded by the chloroplast genome. The characterization and sequencing of a number of algal and plant chloroplast genomes has facilitated researchers understanding of cellular functions and metabolism. Chloroplast DNA (cpDNA) has also been used to determine inter- and intraspecies evolutionary relationships and this organelle offers an alternative means of expressing foreign genes. Although a number of species' chloroplast genomes have been characterized and sequenced, no previous attempts of this kind have been made for a chloroplast genome of the family Vitaceae. In this study, attempts were made to characterize and partially sequence the chloroplast genome of Vilis vinifera. Chloroplast DNA was isolated from the Sultana and Sugra 1 cultivars and digested with restriction enzymes that produced cpDNA fragments of a suitable size for cloning. The fragments were shotgun-cloned into a plasmid vector and white colonies were screened by means of PCR and colony blotting. Three EcoRI-digested clones and one PstI-digested clone were obtained in this manner. Walking outwards from a previously sequenced grapevine rrn 16 gene region by means of PCR also allowed us to sequence a further -3310 bp region of the Sultana chloroplast genome. BAC clones containing V. vinifera cv L. Cabernet Sauvignon cpDNA inserts became available later in the project. It was decided to use these clones for further library construction instead of isolated cpDNA. The 5' and 3' end sequences of seven of the 24 BAC clones were obtained. These were compared to sequences found in the NCBI database to find - homologous chloroplast regions and determine the size of each BAC insert. One clone appeared to contain the entire grapevine chloroplast genome, apart from a 500 bp region. This clone was selected for further analysis. The BAC clone DNA was isolated and restriction-digested fragments were shotgun-cloned into a plasmid vector. White colonies were screened by isolating the plasmid DNA and digesting it with appropriate restriction enzy~es. The 5' and 3' ends of putative positive clones were sequenced and mapped onto the Atropa belladonna chloroplast genome. A total of 15 clones were obtained in this project. Five of these contain cpDNA isolated from grapevine leaves and 10 contain fragments sub-cloned from the BAC clone. The biggest problem encountered with both methods used for library construction was genomic DNA contamination. Genomic DNA either originated from the plant nuclear genome or from the bacterial host cells in which the BAC clones were maintained. Many of the clones screened contained genomic DNA, and these could only be identified and removed once the clones had been sequenced. Even when a commercial kit was used for BAC clone isolation, 31% of the clones screened contained genomic DNA. This kit was specifically designed for the isolation of genomic DNA-free large constructs. The clones obtained from the two strategies provided a good representation of the grapevine chloroplast genome. The only region not represented was the Small Single Copy (SSC) region. Approximately 40% of the grapevine chloroplast genome was covered by these clones. This provides a basis for further genome characterization, physical mapping and sequencing of the grapevine chloroplast genome.
AFRIKAANSE OPSOMMING: Die chloroplasgenoom kodeer VIr 'n hele aantal proteïene wat essensieel is VIr die voortbestaan van 'n plant. Die karakterisering en volgorde bepaling van 'n aantal alg en plant chloroplasgenome het dit. vir navorsers moontlik gemaak om sellulêre funksies en metabolisme van plante te ontrafel. Chloroplas DNA (cpDNA) is ook gebruik om intra- en interspecies evolusionêre verwantskappe vas te stel. Dié organel verskaf ook 'n alternatiewe manier vir die uitdrukking van transgene. Alhoewel die chloroplasgenome van 'n hele aantal species al gekarakteriseer is en die DNA volgorde daarvan bepaal is, is daar nog geen navorsing van bogenoemde aard op die chloroplasgenoom van die Vitaceae familie gedoen rue. In hierdie studie is beoog om die chloroplasgenoom van Vitis vinifera te karakteriseer en gedeeltelike volgordebepaling daarvan te doen. Chloroplas DNA is geïsoleer vanaf Sultana en Sugra 1 kultivars en restriksie-ensiem vertering is gedoen met ensieme wat cpDNA fragmente, met geskikte grootte vir klonering, produseer. Dié fragmente is in 'n plasmiedvektor gekloneer met die haelgeweer-metode en wit kolonies is gesif deur middel van PKR en die kolonieklad metode. Op hierdie manier is drie EcoRI-verteerde klone en een PstI-verteerde kloon verkry. Deur uitwaarts te loop, deur middel van PKR, vanaf 'n druif rrnl6 geenstreek, waarvan die volgorde voorafbepaal is, was dit vir ons moontlik om ook die volgorde te bepaal van 'n verdere ~3310 bp streek van die Sultana chloroplasgenoom. BAC klone wat V. vinifera cv L. Cabernet Sauvignon cpDNA fragmente bevat, het later in die projek beskikbaar geraak. Daar is besluit om hierdie klone, i.p.v. die geïsoleerde cpDNA, te gebruik vir verdere biblioteek konstruksie. Die 5' en 3' entpuntvolgordes van sewe uit die 24 BAC ~lone is verkry. Hierdie volgordes is vergelyk met volgordes in die NCB Idatabasis om homoloë chloroplas streke te identifiseer, en die grootte van elke BAC fragment te bepaal. Die het geblyk dat die hele druif chloroplasgenoom in een van die klone vervat is, behalwe vir 'n 500 bp streek. Die BAC-kloon DNA is geïsoleer en die restriksie-verteerde fragmente is in 'n plasmiedvektor gekloon d.m.V. die haelgeweer-metode. Wit kolonies is gesif deur die isolering van plasmied DNA en die vertering daarvan met geskikte restriksie-ensieme. Die volgorde van die 5' en 3' entpunte van skynbare positiewe klone is bepaal en gekarteer op die Atropa belladonna chloroplasgenoom. In hierdie studie is 'n totaal van 15 klone verkry. Vyf hiervan bevat cpDNA wat vanaf druifblare geïsoleer is, en 10 bevat fragmente wat vanaf die BAC-klone gesubkloneer is. Genorniese DNA kontaminasie was die grootste probleem wat ondervind is tydens beide metodes wat gebruik is vir biblioteek konstruksie. Genomiese DNA was afkomstig vanaf óf die plant nukleêre genoom óf die bakteriële gasheerselle waarin die BAC-klone gehou is. Baie van die klone wat gesif is, het genomiese DNA bevat, en dit kon eers geïdentifiseer en verwyder word nadat die volgorde van die klone bepaal is. Selfs al is 'n kommersiële produk vir BAC-kloon isolasie gebruik, het 31% van die gesifde klone steeds genomiese DNA bevat. Dié kommersiële produk is spesifiek vir die isolasie van groot konstrukte, wat genomiese DNA vry is, ontwerp. Die klone wat deur die twee strategeë verkry is, het 'n goeie verteenwoordiging van die druif chloroplasgenoom gegee. Die enigste streek wat die verteenwoordig is nie, was die Klein Enkelkopie (SSC) streek. Ongeveer 40% van die druif chloroplasgenoom is deur hierdie klone gedek. Dit verskaf 'n basis vir verdere genoomkarakterisering, fisiese kartering en volgordebepaling van die druif chloroplasgenoom.
Lin, Cheng-Hsien Kenny. "An ASIC application for DNA sequencing by Smith-Waterman algorithm (DNASSWA) /". [St. Lucia, Qld.], 2004. http://www.library.uq.edu.au/pdfserve.php?image=thesisabs/absthe18716.pdf.
Pełny tekst źródłaYuwaraj, Murugathas. "A local processor for improving the accuracy of automated DNA sequencing". Thesis, National Library of Canada = Bibliothèque nationale du Canada, 2001. http://www.collectionscanada.ca/obj/s4/f2/dsk3/ftp05/NQ63645.pdf.
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