Global ETD Search
Search theses and dissertations gathered from participating repositories worldwide. Every result links back to the library that holds it. No account is needed.
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Showing 1 to 16 of 16 for “"Sequence Assembly"”.
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Scaling short read de novo DNA sequence assembly to gigabase genomes
… and more varied error rates. Modern genome assembly tools compensate for these shortcomings by using de Bruijn graph based assembly techniques; however, for large genomes, the physical memory required to efficiently build and manipulate the de Bruijn graph generally far exceeds that which is …
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Probabilistic insertion, deletion and substitution error correction using Markov inference in next generation sequencing reads
… of noisy reads obtained from high-throughput DNA sequencers is an important problem since read quality significantly affects downstream analyses such as detection of genetic variation and the complexity and success of sequence assembly. Most of the current error correction algorithms are only …
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Tiger: tiled iterative genome assembler and approximate multi-genome aligner
Sequence assembly and alignments are two important stepping stones for comparative genomics. With the fast adoption of the next-generation sequencing (NGS) technologies and the coming of the third-generation sequencing (TGS) technologies, genomics has provided us with an unprecedented opportunity …
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Complete computational sequence characterization of mobile element variations in the human genome using meta-personal genome data
… been developed to detect such types of genome sequence variations as single nucleotide polymorphisms (SNPs) and small indels, comparatively fewer methods have been developed for finding structural variants (SVs) and in particular mobile elements insertions (MEIs). Moreover, almost all these …
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Improved plastid transformation in Marchantia polymorpha
… improved by the generation of the first plastome sequence assembly for a widely used laboratory strain of Marchantia, optimisation of the transformation protocol itself, and a comparison of the in vivo activity of plastid regulatory elements through a fluorescent marker and quantitative …
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Estudos de imunobioinformática e imunoprofilático de uma proteína de fusão contra a infecção por Corynebacterium pseudotuberculosis em modelo murino
… tools for the construction of the amino acid sequence, assembly and validation of the 3D structure, physicochemical analysis, antigenicity and allergenic potential, prediction of B lymphocytes specific epitopes and those capable of binding to molecules of the complex major histocompatibility …
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Identification of genes involved in (1,3;1,4)-β-glucan synthesis in barley (<i>Hordeum vulgare</i>)
… remain unclear. Using the barley Morex genome sequence assembly, new genes of the CslF family (HvCslF11 and HvCslF12) were identified and tested for a potential function in (1,3;1,4)-β-glucan biosynthesis using a transient expression system in Nicotiana benthamiana. This analysis highlighted …
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EPSPS gene duplication in Palmer amaranth: relative fitness, inheritance, and duplication mechanism of the glyphosate resistance trait
… the mechanism of EPSPS gene duplication through sequence assembly of the EPSPS amplicon and chromosomal localization of this duplicated region. The amplicon was extended out to a little over 110kb and was found to contain mostly repetitive sequence including long direct repeats, microsatellites, …
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Microbial profiling using metagenomic assembly
… diversity. The explosive growth of microbial sequence data has also necessitated advances in bioinformatic methods for profiling microbial communities. Data aggregation strategies should allow the relation of metagenomic sequence data to our understanding of microbial taxonomy, while also …
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PARSES: A Pipeline for Analysis of RNA-Sequencing Exogenous Sequences
… PARSES, a pipeline constructed from existing sequence analysis tools, which allows the user to interrogate RNA-Sequencing experiments for possible biological contamination or the presence of exogenous sequences that may shed light on other factors influencing an organism's condition.
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MR-CUDASW - GPU accelerated Smith-Waterman algorithm for medium-length (meta)genomic data
… In this thesis an existing GPU-accelerated sequence alignment algorithm is adapted and expanded to reduce its completion time. A number of improvements and changes are made to the original software. Workload distribution, query profile construction, and thread scheduling techniques …
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Identification of acyl transferases responsible for the diverse hydroxycinnamoyl chemical space in bidens pilosa
… of long reads which overcomes the challenges of sequence assembly synonymous with the short reads achieved by the former two sequencing approaches. Moreover, this technique allows detection of isoforms of a specific gene, caused by either inherited genetic code or alternative splicing events. …
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Analysis of the antifreeze glycoprotein containing genomic locus in the Antarctic notothenioid fish dissostichus mawsoni
… two haplotypes encompassed the AFGP/TLP locus. Assembly of the AFGP/TLP locus was complicated by its highly repetitive nature. Thus, an assembly protocol was developed which entailed construction of subclone libraries of two insert size ranges (1-5 kbp and 5-30 kbp) for some of the positive BAC …
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Genetic characterization of Rpp1-mediated Asian soybean rust resistance using in-depth transcriptomic and genomic analyses
… fosmid libraries were constructed, screened and sequenced, and a whole genome sequence assembly were conducted on TMG06_0011 using the new 10X Genomics technology. Due to the lack of biological replications, the statistical analysis of differential expressed genes was computed by combining the …
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Creating sense from non-sense DNA: de novo genesis and evolutionary history of antifreeze glycoprotein gene in northern cod fishes (gadidae)
… unknown, as thus far there are no homologous sequences in databases to infer genetic ancestry based on sequence homology. Additionally, the seven AFGP-bearing species are dispersed in separate clades of the gadid phylogeny, indicating a complicated evolutionary history of AFGP in the gadid …
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An investigation into the fundamental understanding of an activated sludge bioremediation process and optimisation of thiocyanate and cyanide destruction
… genes, of which 106 non-identical genotypes were sequenced. In contrast, for the reactor containing solids, only 48 representatives were selected and 30 genotypes were sequenced. Bacteria implicated in SCN destruction in the reactor containing suspended solids were members from the genera Bosea, …