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.
Results
Showing 1 to 20 of 84 for “"reference genome"”.
-
Towards cloning of a novel SCN resistance locus using de novo genome assembly and fosmid screening
… to a distance of 147kb. Through the use of whole genome sequencing with de novo assembly we were able to gain information about the region. In this thesis the assembly data was used along with fosmid sequences from both Sanger sequencing and Illumina reads to gain insight into sequence differences …
-
Chromosomal assembly and comparative analysis of the red fox (Vulpes vulpes) genome
… the early days of genomics, the development of a reference genome was an expensive, collaborative undertaking reserved only for traditional and popular model organisms; however, in a theoretical shift highlighted most clearly by the goals of the Genome 10K Project, the advent of next-generation …
-
Creating and analysing an African pan-genome
The human reference genome is currently a core resource for understanding the role of genetics in human health, disease, and variation, and has been invaluable in the development of clinical and computational tools for these purposes. However, the limited number of individual genomes used to create …
-
HUMAN GENOME VARIATIONS AND EVOLUTION WITH A FOCUS ON THE ANALYSIS OF TRANSPOSABLE ELEMENTS
Genome sequence varies in numerous ways among individuals although the gross architecture is fixed for all humans. Retrotransposons create one of the most abundant structural variants in the human genome and are divided in many families, with certain members in some families, e.g., L1, Alu, SVA, …
-
CHROMOSOME-LEVEL DE NOVO GENOME ASSEMBLIES OF AVIAN SPECIES AND THEIR RELEVANCE FOR COMPARATIVE GENOMICS, PANGENOMICS, POPULATION GENOMICS AND SPECIES CONSERVATION.
… have been limited by the lack of complete reference genomes, thus having to focus on a limited number of genes or incomplete genomic sequencing data. In several cases, this led to wrong or incomplete assumptions and to conservation decisions which did not carry the desired effects due to …
-
Genic copy number variation associated with abiotic/biotic stress among a set of progenitors of contemporary maize germplasm
… it is estimated that a greater portion of the genome is affected by structural variation (SV). This is a broad phenomenon that includes copy number variation (CNV), inversions, and translocations that affect an intermediate-scale of genomic sequence. Structural variation has the potential to …
-
Graphical pangenomics
Completely sequencing genomes is expensive, and to save costs we often analyze new genomic data in the context of a reference genome. This approach distorts our image of the inferred genome, an effect which we describe as reference bias. To mitigate reference bias, I repurpose graphical models …
-
FPGA acceleration of short read alignment with high-level synthesis
… fragments of DNA to the large and expansive reference genome. This can be a very time-consuming process with much room for improvement. This thesis improves on Bowtie 2, an aligner that is already very popular and high-performing. Through the use of OpenCL, it is possible to parallelize this …
-
Transcript Diversity In The Protozoan Parasite Toxoplasma Gondii
… Such information permits refinement of draft genome annotation originally generated in the absence of transcript coverage data, and provides new insights into organismal biology and regulatory mechanisms. This dissertation provides an extensive analysis of mRNA-seq data from the obligate …
-
Navigating through the uncertainty of genotyping-by-sequencing data in polyploids
… autopolyploids but for a species with a complex genome, such as sugarcane, the level of uncertainty within GBS data increases making trait mapping difficult. Furthermore, variant and genotype calling methods remain a challenge for both recent and ancient allopolyploids (e.g. wheat, maize, …
-
Mapping Bisulfite-Treated Short DNA Reads
… The resulting sequences can be mapped to a reference genome; however, this can be challenging due to sequencing technology complexity, low sequence complexity, and biases and errors introduced with bisulfite treatment. Once the short read is mapped, the identity of 5-methylcytosine or …
-
Insights into the genomic histories of diverse human populations using whole-genome sequencing analysis.
… 54 human populations which are part of the Human Genome Diversity Project (HGDP-CEPH) panel. Using whole-genome sequences previously produced at the Wellcome Sanger Institute, I generated a comprehensive catalogue of structural variation identifying a total of 126,018 variants, of which 78% are …
-
PARSES: A Pipeline for Analysis of RNA-Sequencing Exogenous Sequences
… of mapping reads back to the host organism's genome [2] [3]. This allows for analysis of most reads produced by the experiments, but these tools typically discard reads that do not match well with the reference genome. This additional information could reveal important insight into the …
-
Computational Pipeline for Human Transcriptome Quantification Using RNA-seq Data
… alignment of a large volume of short reads to a reference genome is a key step in NGS data analysis. Although storing alignment information in the Sequence Alignment/Map (SAM) or Binary SAM (BAM) format is now standard, biomedical researchers still have difficulty accessing useful information. In …
-
Exact genome alignment
… data due to the decrease in the cost of whole genome sequencing techniques has opened up new avenues of research in the field of Bioinformatics, like comparative genomics and evolutionary dynamics. The fundamental task in these studies is to align the genome sequences accurately. Sequence …
-
Performance comparison of five RNA-seq alignment tools
Aligning millions of short reads to a reference genome is a critical task in high throughput sequencing. In recent years, a large number of mapping algorithms have been developed, all of which have in common that they align a vast number of reads to genomic or transcriptomic sequences. RNA-Seq data …
-
The developmental liver transcriptome of Rattus norvegicus
… a bioinformatics approach to improve upon the reference annotation for known genes. Our research gives insight to the biological phenomenon of late gestational and post parturition liver development. Additionally, we provided annotation for over 1000 regions in the rat reference genome. Further …
-
Comparative and Epidemiological Genomics of Human Malaria Parasites
… the genomic basis of malaria biology, the genome sequences of two of the five human malaria parasite species, Plasmodium malariae and P. ovale, have remained essentially a mystery. Consequently, the implications of these sequences on aspects such as drug resistance have eluded us. However, …
-
Empirical accuracy bounds for next-generation sequencing variant calling workflows
… uniquely mapped to every position of the human reference genome, so errors are inevitable. We will analyze the repetitive content of several organisms, and estimate the maximum attainable alignment accuracy as a function of read length. Additionally, we will show that paired-end sequencing with …
-
Dissection of black rot resistance towards marker-assisted breeding in grapevine Pedigree reconstruction and phenotyping optimization coupled with high-density linkage mapping revealed a major QTL associated with bunch resistance.
… it from 2.4 to 0.7 Mb along the PN40024.v4 reference genome. The region resulted enriched in genes belonging to phloem dynamics and mitochondrial pro-ton transfer. The second QTL associated with bunch resistance was designated Rgb3. Located at 9 cM (6 Mb) upstream Rgb1, it was characterized …
Page 1 of 5