Dissertations / Theses: 'Nucleotide sequence'

1

Wang, Zhenggang. "Improved algorithm for entropic segmentation of DNA sequence /." View abstract or full-text, 2004. http://library.ust.hk/cgi/db/thesis.pl?PHYS%202004%20WANG.

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Thesis (M. Phil.)--Hong Kong University of Science and Technology, 2004.
Includes bibliographical references (leaves 56-58). Also available in electronic version. Access restricted to campus users.

2

Siu, Kim-Man. "A computational estimation of errors in model genomes using exactly duplicated DNA sequences /." View abstract or full-text, 2005. http://library.ust.hk/cgi/db/thesis.pl?MATH%202005%20SIU.

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3

Ngwira, Patricia. "Nucleotide sequence diversity in maize and grass-infecting streak geminiviruses: A basis for nucleotide sequence classification and identification /." The Ohio State University, 1997. http://rave.ohiolink.edu/etdc/view?acc_num=osu1487945015618607.

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4

Cai, Zheng. "Repetitive sequence analysis for soybean genome sequences." Diss., Columbia, Mo. : University of Missouri-Columbia, 2005. http://hdl.handle.net/10355/4249.

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Thesis (M.S.)--University of Missouri-Columbia, 2005.
"May 2005" The entire dissertation/thesis text is included in the research.pdf file; the official abstract appears in the short.pdf file (which also appears in the research.pdf); a non-technical general description, or public abstract, appears in the public.pdf file. Includes bibliographical references.

5

Huckle, James William. ""Prokaryotic Metallothionein gene isolation, Nucleotide sequence and expression"." Thesis, Durham University, 1993. http://etheses.dur.ac.uk/5662/.

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Metallothioneins (MTs) are low molecular weight, cysteine-rich, metal-binding proteins, which are proposed to have roles in essential trace metal homoeostasis and in the detoxification of metal ions. The genes encoding MTs have been isolated from a wide range of eukaryotes, although MT genes have not previously been isolated from prokaryotes. The polymerase chain reaction (PGR) was initially used to isolate a prokaryotic MT gene fragment from Synechococcus PCC 6301. PGR fragments were amplified using inosine-containing primers designed from the amino acid sequence of a prokaryotic MT. Subsequent cloning and nucleotide sequence analysis revealed that the deduced amino acid sequence of the PGR product corresponded to the amino acid sequence of the prokaryotic MT. The amplified product was thus part of the gene encoding the MT, and was designated smtA. The same primers used in the initial amplification were subsequently utilised for anchored PGR, to amplify the remainder of the coding region and the 3' and 5' flanking regions of the smtA gene. A genomic library was produced from Synechococcus PGG 7942 DNA and screened using the PGR products described above as probes. A genomic clone was isolated, nucleotide sequence analysis revealed the structure of the smt locus, two open reading frames, smtA and smtB, arranged in a divergent orientation about the smt operator/promoter region. The operator/promoter region contains the transcriptional and translational signals for the two genes and three regions that are candidate sites for interaction of regulatory proteins. The transcript start sites of the two genes were mapped within the operator/promoter region by primer extension analysis. An increase in the relative abundance of transcripts of both smt genes was studied in response to various metal ions in a series of northern blots. Inhibitor studies confirmed that the smtA gene is regulated at the transcriptional level. The 5' flanking region of the smtA gene conferred metal specific induction of the reporter gene lacZ. SmtB has sequence similarity to several prokaryotic regulatory proteins and contains a putative helix-turn-helix structural domain. Deletion analysis suggests that SmtB is a repressor of smtA expression. Subsequent work has confirmed that SmtB is a trans-acting repressor of expression from the smt operator/promoter.

6

Earle, John Alexander Philip. "The nucleotide sequence of a bovine enterovirus genome." Thesis, Queen's University Belfast, 1987. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.317112.

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7

Mohamed, Maizan. "Sequence analysis of the small (s) RNA segment of viruses in the genus Orthobunyavirus." Thesis, St Andrews, 2007. http://hdl.handle.net/10023/434.

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8

Musgrave-Brown, Esther. "Development and application of methods for targeted DNA sequencing of pooled samples." Thesis, University of Cambridge, 2014. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.648613.

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9

Cheng, Kai-hong. "Further development of the visual genome explorer a visual genomic comparative tool /." Hong Kong : University of Hong Kong, 2001. http://sunzi.lib.hku.hk/hkuto/record.jsp?B23242437.

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10

Halsall, John Richard. "Isolation and characterisation of the B42 mating type locus of Coprinus cinereus." Thesis, University of Oxford, 1997. http://ora.ox.ac.uk/objects/uuid:d5340e8b-29d7-4418-be27-f0c06e10ca18.

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C. cinereus, any two of which are sufficient to promote B-regulated development following cell fusion. The isolation of the B42 locus is described along with the DNA sequence analysis that identified nine B mating type genes within a 27kb B42 -specific DNA sequence. Six of the genes, with small transcripts of 800-900nt, encode the mating pheromone precursors and the other three, with 1.9 to 2-5kb transcripts, encode the transmembrane pheromone receptors. The genes are arranged in three groups, designated group 1, 2 and 3, each consisting of one receptor gene and two pheromone genes. B42 and B6 share the same alleles of the group 1 genes, but not those of groups 2 and 3. This was demonstrated by DNAsequence analysis and Southern blot analysis. None of the group 1 genes from B42 were able to activate B -regulated development in a B6 host when introduced by transformation but with one exception, all genes from group 2 and group 3 were able to do so. This analysis led to the recognition that the three genes in any one group are held together in an allele-specific DNA sequence and that Southern blot analysis and transformation can be used to identify shared alleles in uncloned loci. Extensive Southern analyses using cloned genes to probe genomic DNAs from strains having other B mating specificites showed that different B loci may share identical alleles of two groups of genes. Mating partners thus require different alleles of only one group of genes to generate a compatible B mating interaction. Transformation analyses with the same cloned genes confirmed the conclusions derived from the hybridisation data. Multiple B mating specificities thus appear to be derived from three groups of multiallelic and functionally redundant genes. A tenth gene located within the B42- specific DNA sequence encodes a putative transporter protein belonging to the major facilitator superfamily (MFS). In other genomic backgrounds this gene lies in homologous flanking sequences and its presence within the B42 locus is unlikely to be related to mating type function.

11

Alley, Stephen Charles. "The sequence-dependence of DNA flexibility /." Thesis, Connect to this title online; UW restricted, 1996. http://hdl.handle.net/1773/8678.

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12

Eubanks, Aleida C. (Aleida Christine). "Nucleotide Sequence of a Bovine Arginine Transfer RNA Gene." Thesis, University of North Texas, 1996. https://digital.library.unt.edu/ark:/67531/metadc278753/.

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A single plaque-pure lambda clone designated λBA84 that hybridized to a ˆ32P-labeled bovine arginine tRNA was isolated from a bovine genomic library harbored in a lambda bacteriophage vector. A 2.3-kilobase segment of this clone was found to contain an arginine transfer RNAccg gene by Southern blot hybridization analysis and dideoxyribonucleotide DNA sequencing. This gene contains the characteristic RNA polymerase III split promoter sequence found in all eukaryotic tRNAs and a potential RNA polymerase III termination site, consisting of four consecutive thymine residues, in the 3'-flanking region. Several possible cis-acting promoter elements were found within the 5'-flanking region of the sequenced gene. The function of these elements, if any, is unknown.

13

Didelot, Xavier. "Inference of bacterial microevolution from large scale DNA sequence datasets." Thesis, University of Oxford, 2007. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.670148.

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14

Coles, Leeanne Susan. "Chicken histone H1 genes /." Title page, table of contents and summary only, 1986. http://web4.library.adelaide.edu.au/theses/09PH/09phc693.pdf.

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15

Kam, Sin-yee. "Application of 16S rRNA gene sequencing in laboratory diagnosis of mycobacteria other than tuberculosis." Click to view the E-thesis via HKUTO, 2003. http://sunzi.lib.hku.hk/hkuto/record/B31971052.

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16

Christensen, Shawn A. "Assessment of Chenopodium quinoa Willd. genetic diversity in the USDA and CIP-FAQ collections using SSR's and SNP's /." Diss., CLICK HERE for online access, 2005. http://contentdm.lib.byu.edu/ETD/image/etd1118.pdf.

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17

金倩儀 and Sin-yee Kam. "Application of 16S rRNA gene sequencing in laboratory diagnosis of mycobacteria other than tuberculosis." Thesis, The University of Hong Kong (Pokfulam, Hong Kong), 2003. http://hub.hku.hk/bib/B31971052.

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18

Krishnan, Vandhana. "Computational approaches for comparative genomics and transcriptomics using 454 sequencing technology." Pullman, Wash. : Washington State University, 2009. http://www.dissertations.wsu.edu/Thesis/Summer2009/v_krishnan_072409.pdf.

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Thesis (M.S. in computer science)--Washington State University, August 2009.
Title from PDF title page (viewed on Aug. 12, 2009). "School of Electrical Engineering and Computer Science." Includes bibliographical references (p. 80-87).

19

Wang, Xiaofei. "Molecular characterization and cytogenetic analysis of chicken repetitive DNA sequences /." Hong Kong : University of Hong Kong, 1999. http://sunzi.lib.hku.hk/hkuto/record.jsp?B20979393.

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20

Local, Andrea. "Cloning of Carbonic Anhydrase from Cotton (Gossypium hirsutum L.)." Thesis, University of North Texas, 1998. https://digital.library.unt.edu/ark:/67531/metadc279044/.

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Carbonic anhydrase is a ubiquitous zinc-metalloenzyme that catalyzes the interconversion of carbon dioxide and carbonate and has been found to play a wide range of roles in animals, plants and bacteria. Cotton genomic and cDNA libraries were screened for the plastidial isoform of carbonic anhydrase. The nucleotide sequences of two 1.2 Kb partial cDNA clones were determined. These clones exhibit high homology to carbonic anhydrases from other dicot plants and possess all the expected peptide motifs. For example, serine and threonine rich chloroplastic targeting peptide and conserved zinc binding residues are both present. These clones were utilized to isolate two carbonic anhydrase genes that were shown to encode different isoforms by PCR and RFLP analysis.

21

Lee, Hong-seng Daniel, and 李康善. "Foldback DNA: nucleotide sequence and characterization of MboII repeated sequences in human long foldbackDNA by molecular cloning and hybridization." Thesis, The University of Hong Kong (Pokfulam, Hong Kong), 1987. http://hub.hku.hk/bib/B31231251.

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22

Ganapathy, Ashwin. "Computational analysis of protein identification using peptide mass fingerprinting approach /." free to MU campus, to others for purchase, 2004. http://wwwlib.umi.com/cr/mo/fullcit?p1426056.

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23

Ryan, Martin Denis. "Molecular cloning and nucleotide sequence studies on enterovirus type 70." Thesis, University of Leicester, 1985. http://hdl.handle.net/2381/35415.

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The molecular cloning of enterovirus type 70 (EV70) was achieved using the hybrid (vRNA:cDNA) cloning strategy. Recombinant plasmids containing EV70 sequences were identified by hybridization in situ. EV70 cDNAs were characterized by optical and Smith-Birnstie1 (1976) restriction mapping techniques. Hybridization and restriction mapping data showed that a series of overlapping, subgenomic EV70 clones spanning 7.25Kbp had been produced. EV70 cDNAs were isolated and fragmented by subsequent restriction or ultra-sonic shearing methods. cDNA fragments produced by these methods were sub-cloned into bacteriophage M13 vectors and their nucleotide sequences determined by the dideoxynucleotide chain-termination method (Sanger et al, 1977). The results showed that considerable homology existed between EV70 and poliovirus. The homology was sufficient to permit identification and delineation of EV70 infected-cell polypeptides by analogy with the po1ioviruses. Many aspects of the biology of EV70, therefore, could be correlated with specific regions of the genome.

24

Fullerton, Stephanie Malia. "Allelic sequence diversity at the human beta-globin locus." Thesis, University of Oxford, 1994. http://ora.ox.ac.uk/objects/uuid:da897e20-7dae-4c77-9c4d-0be69cb024e1.

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25

Lee, Hong-seng Daniel. "Foldback DNA : nucleotide sequence and characterization of MboII repeated sequences in human long foldback DNA by molecular cloning and hybridization /." [Hong Kong : University of Hong Kong], 1987. http://sunzi.lib.hku.hk/hkuto/record.jsp?B12263643.

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26

Leung, Chi-ming. "Motif discovery for DNA sequences." Click to view the E-thesis via HKUTO, 2006. http://sunzi.lib.hku.hk/hkuto/record/B3859755X.

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27

Wang, Tai-Chun. "Computational experiment for the solution of single nucleotide polymorphisms (SNPS) problems." Thesis, The University of Sydney, 2011. https://hdl.handle.net/2123/29228.

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Single Nucleotide Polymorphisms (SNPs) have recently received significant attention from researchers in different life science disciplines. The discovery of novel SNPs from expressed sequence tags could be an economical method for researchers when handling those species which do not have complete reference sequences. However, distinguishing sequence errors from putative SNPs is a significant problem for in silico methods. Previous researchers have indicated that series of SNPs from the same chromosome, called haplotypes, contain more information than individual SNPs. Thus, reconstructing individual haplotypes from SNP fragments becomes one of the core problems in whole genome sequencing research. Unfortunately, current methods do not have the ability to efficiently handle high error-rate data sets or longer individual haplotypes. Besides the single individual haplotype reconstruction problem, the tag SNP selection problem is the other haplotype-related application that is currently being focused on by researchers. Tag SNP is a kind of biomarker used to tag haplotypes. However, this has been proven to be a NP-hard problem. This study addresses three SNP-related topics—novel SNP discovery, tag SNP selection and single individual haplotype reconstruction—and presents novel computational methods associated with these areas. When mining SNPs from expressed sequence tag data sets, a fuzzy logic system, in conjunction with several statistical measurements, was used to produce highly reliable results. A pipeline framework which merged the advantages of block-based and LD—based models was introduced for selecting highly correlated tag SNPs. A radix tree-like structure and genetic algorithm were implemented in order to reconstruct the single individual haplotype reconstruction problem based on the minimum error correction strategy. Different species’ data types were used in this study, and the experimental results indicate that our methods provide the best solution for each topic at the present time.

28

Holder, Mark Travis. "Using a complex model of sequence evolution to evaluate and improve phylogenetic methods." Access restricted to users with UT Austin EID Full text (PDF) from UMI/Dissertation Abstracts International, 2001. http://wwwlib.umi.com/cr/utexas/fullcit?p3037500.

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29

Williams, Joseph Paul. "Sequencing and annotation of potential cis-acting transcription elements in the emb-9 gene promoter of caenorhabditis elegans /." MSU Only Available Electronically, 2009. http://purl.missouristate.edu/etd/Williams.Joseph-2009-SP.

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30

Sakamoto, Hidenori, and Yuichi Sasayama. "Nucleotide sequence of cDNA of bone-mineralizing hormone calcitonin in medaka (Teleostei)." Laboratory of Freshwater Fish Stocks Bioscience and Biotechnology Center Nagoya University, 2007. http://hdl.handle.net/2237/13830.

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31

Ng, Siu-Kin. "Lineage specific genomics features and insights into evolutionary pathways /." View abstract or full-text, 2007. http://library.ust.hk/cgi/db/thesis.pl?BIEN%202007%20NG.

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32

招紹裘 and Siu-kau Chiu. "Granulicatella, abiotrophia, and gemella bacteremia characterized by 16S ribosomal RNA gene sequencing." Thesis, The University of Hong Kong (Pokfulam, Hong Kong), 2002. http://hub.hku.hk/bib/B3197045X.

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33

鄭啓航 and Kai-hong Cheng. "Further development of the visual genome explorer: a visual genomic comparative tool." Thesis, The University of Hong Kong (Pokfulam, Hong Kong), 2001. http://hub.hku.hk/bib/B3122412X.

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34

Yeung, Shiu-yan, and 楊兆恩. "Update and evaluation of 16SpathDB, an automated comprehensive database for identification of medically important bacteria by 16S rRNA gene sequencing." Thesis, The University of Hong Kong (Pokfulam, Hong Kong), 2013. http://hdl.handle.net/10722/193552.

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Identification of pathogens is one of the important duties of clinical microbiology laboratory. Traditionally, phenotypic tests are used to identify the bacteria. However, due to some limitations of the phenotypic tests, the bacteria may not be identified sometimes and cannot be identified promptly. 16S rRNA gene sequencing is a rapid and accurate method to achieve this target. It is especially useful for identify rare or slow growing bacteria. However, the interpretation of the 16S rRNA gene sequencing result is one of the challenging duties to laboratory technicians and microbiologists. Apart from the well known 16S rRNA gene databases such as Genbank, The Ribosomal Database Project (RDP-II), MicroSeq databases, Ribosomal Differentiation of medical Microorganism database (RIDOM), SmartGene IDNS, 16SpathDB is an automated and comprehensive database for interpret the 16S rRNA gene result. The 16SpathDB first version was established in 2011. In this study, 16SpathDB was updated based on the all clinical important bacteria present in the 10th edition of the Manual of Clinical Microbiology (MCM)(Versalovic. et al., 2011) into this new version of database, 16SpathDB 2.0. The database was evaluated by using 689 16S rRNA gene sequences from 689 complete genomes of medically important bacteria. Among the 689 16S rRNA gene sequences, none was wrongly identified by 16SpathDB 2.0, with 247 (35.8%) 16S rRNA gene sequences reported in only one single bacterial species with more than 98% nucleotide identity with the query sequence (category 1), 440 (63.9%) reported as more than one bacterial species having more than 98% nucleotide identity with the query sequence (category 2), 2 (0.3%) reported to the genus level (category 3), and none reported as “no species in 16SpathDB 2.0 found to be sharing high nucleotide identity to your query sequence” (category 4). 16SpathDB 2.0 is an updated, automated, user-friendly, efficient and accurate database for 16S rRNA gene sequence interpretation in clinical microbiology laboratories.
published_or_final_version
Microbiology
Master
Master of Medical Sciences

35

Li, Yaoman, and 李耀满. "Efficient methods for improving the sensitivity and accuracy of RNA alignments and structure prediction." Thesis, The University of Hong Kong (Pokfulam, Hong Kong), 2013. http://hdl.handle.net/10722/195977.

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RNA plays an important role in molecular biology. RNA sequence comparison is an important method to analysis the gene expression. Since aligning RNA reads needs to handle gaps, mutations, poly-A tails, etc. It is much more difficult than aligning other sequences. In this thesis, we study the RNA-Seq align tools, the existing gene information database and how to improve the accuracy of alignment and predict RNA secondary structure. The known gene information database contains a lot of reliable gene information that has been discovered. And we note most DNA align tools are well developed. They can run much faster than existing RNA-Seq align tools and have higher sensitivity and accuracy. Combining with the known gene information database, we present a method to align RNA-Seq data by using DNA align tools. I.e. we use the DNA align tools to do alignment and use the gene information to convert the alignment to genome based. The gene information database, though updated daily, there are still a lot of genes and alternative splicings that hadn't been discovered. If our RNA align tool only relies on the known gene database, then there may be a lot reads that come from unknown gene or alternative splicing cannot be aligned. Thus, we show a combinational method that can cover potential alternative splicing junction sites. Combining with the original gene database, the new align tools can cover most alignments which are reported by other RNA-Seq align tools. Recently a lot of RNA-Seq align tools have been developed. They are more powerful and faster than the old generation tools. However, the RNA read alignment is much more complicated than other sequence alignment. The alignments reported by some RNA-Seq align tools have low accuracy. We present a simple and efficient filter method based on the quality score of the reads. It can filter most low accuracy alignments. At last, we present a RNA secondary prediction method that can predict pseudoknot(a type of RNA secondary structure) with high sensitivity and specificity.
published_or_final_version
Computer Science
Master
Master of Philosophy

36

Wang, Weixin, and 王煒欣. "A fast and accurate model to detect germline SNPs and somatic SNVs with high-throughput sequencing." Thesis, The University of Hong Kong (Pokfulam, Hong Kong), 2014. http://hdl.handle.net/10722/197115.

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The rapid development of high-throughput sequencing technology provides a new chance to extend the scale and resolution of genomic research. How to efficiently and accurately call genetic variants in single base level (germline single nucleotide polymorphisms (SNPs) or somatic single nucleotide variants (SNVs)) is the fundamental challenge in sequencing data analysis, because these variants reported to influence transcriptional regulation, alternative splicing, non-coding RNA regulation and protein coding. Many applications have been developed to tackle this challenge. However, the shallow depth and cellular heterogeneity make those tools cannot attain satisfactory accuracy, and the huge volume of sequencing data itself cause this process inefficient. In this dissertation, firstly the performance of prevalent reads aligners and SNP callers for second-generation sequencing (SGS) is evaluated. And due to the high GC-content, the significantly lower coverage and poorer SNP calling performance in the regulatory regions of human genome by SGS is investigated. To enhance the capability to call SNPs, especially within the lower-depth regions, a fast and accurate SNP detection (FaSD) program that uses a binomial distribution based algorithm and a mutation probability is proposed. Based on the comparison with popular software and benchmarked by SNP arrays and high-depth sequencing data, it is demonstrated that FaSD has the best SNP calling accuracy in the aspects of genotype concordance rate and AUC. Furthermore, FaSD can finish SNP calling within four hours for 10X human genome SGS data on a standard desktop computer. Lastly, combined with the joint genotype likelihoods, an updated version of FaSD is proposed to call the cancerous somatic SNVs between paired tumor and normal samples. With extensive assessments on various types of cancer, it is demonstrated that no matter benchmarked by the known somatic SNVs and germline SNPs from database, or somatic SNVs called from higher-depth data, FaSD-somatic has the best overall performance. Inherited and improved from FaSD, FaSD-somatic is also the fastest somatic SNV caller among current programs, and can finish calling somatic mutations within 14 hours for 50X paired tumor and normal samples on normal server.
published_or_final_version
Biochemistry
Doctoral
Doctor of Philosophy

37

Wang, Yi, and 王毅. "Binning and annotation for metagenomic next-generation sequencing reads." Thesis, The University of Hong Kong (Pokfulam, Hong Kong), 2014. http://hdl.handle.net/10722/208040.

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The development of next-generation sequencing technology enables us to obtain a vast number of short reads from metagenomic samples. In metagenomic samples, the reads from different species are mixed together. So, metagenomic binning has been introduced to cluster reads from the same or closely related species and metagenomic annotation is introduced to predict the taxonomic information of each read. Both metagenomic binning and annotation are critical steps in downstream analysis. This thesis discusses the difficulties of these two computational problems and proposes two algorithmic methods, MetaCluster 5.0 and MetaAnnotator, as solutions. There are six major challenges in metagenomic binning: (1) the lack of reference genomes; (2) uneven abundance ratios; (3) short read lengths; (4) a large number of species; (5) the existence of species with extremely-low-abundance; and (6) recovering low-abundance species. To solve these problems, I propose a two-round binning method, MetaCluster 5.0. The improvement achieved by MetaCluster 5.0 is based on three major observations. First, the short q-mer (length-q substring of the sequence with q = 4, 5) frequency distributions of individual sufficiently long fragments sampled from the same genome are more similar than those sampled from different genomes. Second, sufficiently long w-mers (length-w substring of the sequence with w ≈ 30) are usually unique in each individual genome. Third, the k-mer (length-k substring of the sequence with k ≈ 16) frequencies from reads of a species are usually linearly proportional to that of the species’ abundance. The metagenomic annotation methods in the literatures often suffer from five major drawbacks: (1) unable to annotate many reads; (2) less precise annotation for reads and more incorrect annotation for contigs; (3) unable to deal with novel clades with limited references genomes well; (4) performance affected by variable genome sequence similarities between different clades; and (5) high time complexity. In this thesis, a novel tool, MetaAnnotator, is proposed to tackle these problems. There are four major contributions of MetaAnnotator. Firstly, instead of annotating reads/contigs independently, a cluster of reads/contigs are annotated as a whole. Secondly, multiple reference databases are integrated. Thirdly, for each individual clade, quadratic discriminant analysis is applied to capture the similarities between reference sequences in the clade. Fourthly, instead of using alignment tools, MetaAnnotator perform annotation using k-mer exact match which is more efficient. Experiments on both simulated datasets and real datasets show that MetaCluster 5.0 and MetaAnnotator outperform existing tools with higher accuracy as well as less time and space cost.
published_or_final_version
Computer Science
Doctoral
Doctor of Philosophy

38

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.

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39

Van, Der Merwe Pieter de Wet. "UCTD." Thesis, Stellenbosch : Stellenbosch University, 2015. http://hdl.handle.net/10019.1/96877.

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Thesis (MSc)--Stellenbosch University, 2015.
ENGLISH ABSTRACT: Zygophyllum orbiculatum Welwitsch ex Oliv. from Angola and Zygophyllum stapffii Schinz from Namibia were described in the late 1800’s. Recent comparisons of these two species revealed that they were morphologically very similar except that Zygophyllum orbiculatum has unifoliolate leaves and Zygophyllum stapffii has bifoliolate leaves. The similarity of these two species was investigated using nuclear ITS (Internal Transcribed Spacer, i.e. ITS1, 5.8SrDNA, ITS2) region sequence data as phylogenetic markers. Due to almost identical sequences and phylogenetic grouping, it was concluded that they were conspecific. However, the phylogenetic relationships of the major groups within the subfamily Zygophylloideae based on ITS sequences, were unresolved and unsupported, as was found in previous studies using chloroplast gene marker sequences. To resolve the phylogenetic relationships of the major groups within the subfamily Zygophylloideae, a next generation sequencing (NGS) approach was taken. Chloroplasts of taxa representing the major groups within the subfamily were isolated and chloroplast genome sequence data were generated using the Ion Torrent™ sequencer. Additional nuclear ITS cassette data (18SrDNA, ITS1, 5.8SrDNA, ITS2, 26SrDNA) were generated as a by-product and used to produce a large combined aligned sequence matrix for phylogenetic analysis. Model-based phylogenetic programs were able to retrieve strongly supported and resolved phylogenetic relationships of the major groups within Zygophylloideae. Two basal groupings were retrieved in the subfamily. The first grouping consisted of the genera Tetraena, Fagonia and Melocarpum. The second grouping consisted of the monotypic genus Augea and Zygophyllum orbiculatum/stapffii which were embedded within the genus Roepera. Using a gene duplication approach, the chloroplast marker data of genus Zygophyllum sensu stricto placed this genus basal to the Augea, Zygophyllum orbiculatum/stapffii, Roepera clade whilst the nuclear marker data of Zygophyllum sensu stricto, was found in a basal position to the entire subfamily. From this it is concluded that Zygophyllum sensu stricto shows evidence of incomplete lineage sorting. A revised taxonomy for the entire subfamily Zygophylloideae is proposed.
AFRIKAANSE OPSOMMING: Zygophyllum orbiculatum Welwitsch ex Oliv. uit Angola en Zygophyllum stapffii Schinz van Namibië is in die laat 1800's beskryf. Onlangse vergelykings van hierdie twee spesies het getoon dat hulle morfologies baie eners is, behalwe dat Zygophyllum orbiculatum unifoliolate blare besit en dat Zygophyllum stapffii bifoliolate blare besit. Hierdie ooreenkoms is ondersoek, met behulp van die nukleêre “ITS” (Internal Transcribed Spacer d.w.s. ITS1, 5.8SrDNA, ITS2) DNS-strook volgordedata as filogenetiese merkers. As gevolg van feitlik identiese geenopeenvolgings is bevind dat die twee spesies konspesifiek is. Die filogenetiese verwantskappe van die groot binnegroepe van die subfamilie Zygophylloideae, gebaseer op ITS geenopeenvolgings, was egter onopgelos en nie ondersteun nie, net soos in vorige studies waarin chloroplast geenmerkervolgordes gebruik was. Om die filogenetiese verwantskappe van die groot binnegroepe van die subfamilie Zygophylloideae op te los, was ‘n betreklik nuwe DNS volgordebepalingstegniek, naamlik “Next Generation Sequencing” (NGS), gebruik. Chloroplaste van taksa, wat die groot groepe binne-in die subfamilie verteenwoordig, is geïsoleer en chloroplast genoomdata is gegenereer met behulp van die Ion Torrent ™ (NGS) DNS-volgordebepaler. Bykomend was die nukleêre “ITS”-kasset volgordedata (18SrDNS, ITS1, 5.8SrDNS, ITS2, 26SrDNS) ook as 'n by-produk gegenereer en ook gebruik om 'n groot gesamentlike DNS oplyningmatriks vir filogenetiese doeleindes. Model-gebaseerde filogenetiese programme was in staat was om sterk ondersteuning en opgeloste filogenetiese verwantskappe van die groot groepe binne-in Zygophylloideae te ontravel. Die subfamilier toon twee basale groeperinge. Die eerste groepering bestaan uit die genera Tetraena, Fagonia en Melocarpum. Die tweede groepering bestaan uit die monotipiese genus Augea en Zygophyllum orbiculatum/stapffii, wat ingebed is binne-in die genus Roepera. Deur ‘n geendupliseringsbenadering te gebruik op die DNS geenopeenvolgings van die verteenwoordigende takson van Zygophyllum sensu stricto, is bevind dat die chloroplast DNS volgordes hierdie groep basaal aan ‘n Roepera/Augea/Zygophyllum orbiculatum/stapffii klade plaas, terwyl die nukleêre DNS volgordes hierdie groep basaal aan die hele subfamilie Zygophylloideae plaas. Hieruit is die gevolgtrekking gemaak dat Zygophyllum sensu scricto bewyse van onvolledige afstammelingsortering toon. ‘n Gewysigde taksonomie vir die hele subfamilie Zygophylloideae word voorgestel.

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Shedlock, Andrew M. "Systematics and life history evolution of world anglerfishes (Teleostei: Lophiiformes) : molecular tests of morphological hypotheses /." Thesis, Connect to this title online; UW restricted, 1997. http://hdl.handle.net/1773/5341.

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41

Clevinger, Jennifer Ann. "Systematics of Silphium and its subtribe Engelmanniinae (Asteraceae : Heliantheae) /." Digital version accessible at:, 1999. http://wwwlib.umi.com/cr/utexas/main.

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42

Chan, Yin-leung. "Identification of bacteria with ambiguous biochemical profiles by 16S ribosomal RNA gene sequencing." Hong Kong : University of Hong Kong, 2001. http://sunzi.lib.hku.hk:8888/cgi-bin/hkuto%5Ftoc%5Fpdf?B23373209.

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Chiu, Siu-kau. "Granulicatella, abiotrophia, and gemella bacteremia characterized by 16S ribosomal RNA gene sequencing." Hong Kong : University of Hong Kong, 2002. http://sunzi.lib.hku.hk/hkuto/record.jsp?B25151605.

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44

Mahmoud, Ahmed Abd-Rabbou. "Characterization of repeated DNA sequences in diploid Thinopyrum species /." free to MU campus, to others for purchase, 2004. http://wwwlib.umi.com/cr/mo/fullcit?p3144438.

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45

Bou, Zeidan Nadim Georges. "Human miRNA Sequence Based Variations Database." Scholar Commons, 2014. https://scholarcommons.usf.edu/etd/5350.

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Abstract:

MicroRNAs (miRNAs) are studied as key genetic elements that regulate the gene expression involved in different human diseases. Clinical sequence based variations like copy number variations (CNVs) affect miRNA biogenesis, dosage and target recognition that may represent potentially functional variants and relevant target bindings. To systematically analyze miRNA-related CNVs and their effects on related genes, a user-friendly free online database was developed to provide further analysis of co-localization of miRNA loci with human genome CNV regions. Further analysis pipelines such as miRNA-target to estimate the levels or locations of variations for genetic duplications, insertions or deletions were also offered. Such information could support the simulation of miRNA-target interactions.

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Liakhovitch, Evgueni. "Genetic algorithm using restricted sequence alignments." Ohio : Ohio University, 2000. http://www.ohiolink.edu/etd/view.cgi?ohiou1172598174.

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47

Clarke, David Morgan. "Pyridine nucleotide transhydrogenase of Escherichia coli: nucleotide sequence of the pnt gene and characterization of the enzyme complex." Thesis, University of British Columbia, 1986. http://hdl.handle.net/2429/27044.

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Abstract:

Based on the rationale that Escherichia coli cells harboring plasmids containing the pnt gene would contain elevated levels of enzyme, three clones were isolated bearing the transhydrogenase gene from the Clarke and Carbon colony bank. The three plasmids were subjected to restriction endonuclease analysis. A 10.4-kilobase restriction fragment which overlapped all three plasmids was cloned into pUC13. Examination of several deletion derivatives of the resulting plasmids and subsequent treatment with exonuclease BAL31 revealed that enhanced transhydrogenase expression was localized within a 3.05-kilobase segment. This segment was located at 35.4 min in the E. coli genome. Plasmid pDC21 conferred on its host 70-fold overproduction of transhydrogenase. The protein products of plasmids carrying the pnt gene were examined by sodium dodecyl sulfate-polyacrylamide gel electrophoresis of membranes from cells containing the plasmids and by in vitro transcription/translation of pDC21. Two polypeptides of molecular weights 52,000 and 48,000 were coded by the 3.05-kilobase fragment of pDC21. Both polypeptides were required for expression of transhydrogenase activity. The transhydrogenase was purified from cytoplasmic membranes of E. coli by pre-extraction of the membranes with sodium cholate and Triton X-100, solubilization of the enzyme with sodium deoxycholate in the presence of 1 M potassium chloride, and centrifugation through a 1.1 M sucrose solution. The purified enzyme consists of two subunits, α and β, of molecular weights 52,000 and 48,000. During transhydrogenation between NADPH and 3-acetylpyridine adenine dinucleotide by both the purified enzyme reconstituted into liposomes and the membrane-bound enzyme, a pH gradient is established across the membrane as indicated by the quenching of fluorescence of 9-aminoacridine. It was concluded that E. coli transhydrogenase acts as a proton pump which is regulated primarily by a pH gradient rather than a membrane potential. Treatment of transhydrogenase with N,N'-dicyclohexylcarbodiimide results in an inhibition of proton pump activity and transhydrogenation, suggesting that proton translocation and catalytic activities are obligatorily linked. [¹⁴C]Dicyclohexylcarbodiimide preferentially labelled the a subunit. The transhydrogenase-catalyzed reduction of 3-acetylpyridine adenine dinucleotide by NADPH was stimulated over three-fold by NADH. It was concluded that NADH binds to an allosteric binding site on the enzyme. The nucleotide sequences of the pntA and pntB genes, coding for the transhydrogenase αand β subunits respectively, were established. The molecular masses of 53,906 (α) and 48,667 (β) and the N-terminal sequences of the predicted polypeptides agree well with the data obtained by analysis of the purified subunits. Several hydrophobic regions large enough to span the cytoplasmic membrane were observed for each subunit.
Medicine, Faculty of
Biochemistry and Molecular Biology, Department of
Graduate

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Peng, Yu, and 彭煜. "Iterative de Bruijn graph assemblers for second-generation sequencing reads." Thesis, The University of Hong Kong (Pokfulam, Hong Kong), 2012. http://hub.hku.hk/bib/B50534051.

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Abstract:

The recent advance of second-generation sequencing technologies has made it possible to generate a vast amount of short read sequences from a DNA (cDNA) sample. Current short read assemblers make use of the de Bruijn graph, in which each vertex is a k-mer and each edge connecting vertex u and vertex v represents u and v appearing in a read consecutively, to produce contigs. There are three major problems for de Bruijn graph assemblers: (1) branch problem, due to errors and repeats; (2) gap problem, due to low or uneven sequencing depth; and (3) error problem, due to sequencing errors. A proper choice of k value is a crucial tradeoff in de Bruijn graph assemblers: a low k value leads to fewer gaps but more branches; a high k value leads to fewer branches but more gaps. In this thesis, I first analyze the fundamental genome assembly problem and then propose an iterative de Bruijn graph assembler (IDBA), which iterates from low to high k values, to construct a de Bruijn graph with fewer branches and fewer gaps than any other de Bruijn graph assembler using a fixed k value. Then, the second-generation sequencing data from metagenomic, single-cell and transcriptome samples is investigated. IDBA is then tailored with special treatments to handle the specific issues for each kind of data. For metagenomic sequencing data, a graph partition algorithm is proposed to separate de Bruijn graph into dense components, which represent similar regions in subspecies from the same species, and multiple sequence alignment is used to produce consensus of each component. For sequencing data with highly uneven depth such as single-cell and metagenomic sequencing data, a method called local assembly is designed to reconstruct missing k-mers in low-depth regions. Then, based on the observation that short and relatively low-depth contigs are more likely erroneous, progressive depth on contigs is used to remove errors in both low-depth and high-depth regions iteratively. For transcriptome sequencing data, a variant of the progressive depth method is adopted to decompose the de Bruijn graph into components corresponding to transcripts from the same gene, and then the transcripts are found in each component by considering the reads and paired-end reads support. Plenty of experiments on both simulated and real data show that IDBA assemblers outperform the existing assemblers by constructing longer contigs with higher completeness and similar or better accuracy. The running time of IDBA assemblers is comparable to existing algorithms, while the memory cost is usually less than the others.
published_or_final_version
Computer Science
Doctoral
Doctor of Philosophy

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Gunyuzlu, Paul L. "The nucleotide sequence of the 3' terminus of soybean mosaic virus." Thesis, Virginia Polytechnic Institute and State University, 1987. http://hdl.handle.net/10919/53126.

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The nucleotide sequence of the 3' terminus of soybean mosaic virus (SMV) VA/G1 RNA has been determined by dideoxynucleotide sequencing of oligo(dT) primed cDNA cloned into a pUC19 cloning vector via EcoR1 linkers. One recombinant plasmid, pSMV49, identified by colony and dot-blot hybridization to ¹²⁵I-SMV RNA, contained an insert of 1443 nucleotides and had an open reading frame of 1119 nucleotides terminating 224 nucleotides from the 3' terminal poly(A) tract. The coat protein cistron identified by a glutamine:serine dipeptide cleavage site 792 nucleotides upstream from the termination sequence could potentially code for a 29.8 kDa protein. The amino acid sequence predicted from the nucleotide sequence of this cistron contains regions identical to other potyvirus coat proteins.
Master of Science

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Garrison, Keith Earl. "Nucleotide sequence polymorphism in ancient cultivars of grape (Vitis vinifera L.) /." For electronic version search Digital dissertations database. Restricted to UC campuses. Access is free to UC campus dissertations, 2004. http://uclibs.org/PID/11984.

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Dissertations / Theses on the topic 'Nucleotide sequence'

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