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 20 of 42 for “"genome annotation"”.
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CBK Bacteriophage Genome Annotation and Organization
… phage CbK being the best studied. As no B3 phage genome sequences are currently available in the Genbank, we decided to determine the nucleotide sequence of the CBK genome. Bacteriophage CbK is a double-stranded DNA phage with an extremely large genome size of 203,242 base pairs and a 66.13% GC …
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RNA genome annotation with a focus on T. brucei
… (UTRs) and UTR-indicating patterns in the genome of T. brucei. T. brucei is an interesting organism, and as the cause of African sleeping sickness -- which infects 300,000-500,000 people and a significant number of cattle annually -- is currently the subject of considerable research. Using …
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Design and implementation of bioinformatics tools for large scale genome annotation
The continuous increase of genome sequencing projects produced a huge amount of data in the last 10 years: currently more than 600 prokaryotic and 80 eukaryotic genomes are fully sequenced and publically available. However the sole sequencing process of a genome is able to determine just raw …
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Decoding DNA: scalable genome annotation software, generative AI, and application to the cactus pear genome
The annotation of protein-coding genes from a raw genome assembly involves identifying the sequence regions that are transcribed into mRNA transcripts, spliced, and ultimately translated into protein. Thus, genome annotation is a fundamental task that critically supports systems level biological …
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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 …
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BRIDGE : a bioinformatics software platform for the integration of heterogeneous data from genomic explorations
… number of publicly available prokaryote genomes has led to new demands for bioinformatics software. With the growing amount of information resulting from high-throughput experiments new questions arise that often focus on the comparison of genes, genomes and their expression profiles. …
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Facilitating Pharmacogenetic Association Studies Using an Extensible Genotype Information Management System
Large-scale genome data projects employing automated, high-throughput techniques have led to a deluge of genomic data that necessitate robust informatic solutions. COBRA-DB is an integrated web-based genome information management system that provides storage for pharmacogenomic information …
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Bioinformatics and Next Generation Sequencing: Applications of Arthropod Genomes
… in this thesis describes NGS applications on genome assembly, genome annotation, and comparative genomics, using arthropods as case studies: (1) by sequencing and analyzing the genomes of three Tetranychus spider mites with three completely different feeding behaviors, we uncovered genomic …
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Computational Tools and Analyses for Improved Inference of Variant Effects
… to be protein-coding genes, refining human genome annotation.
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Assembling improved gene annotations in Clostridium acetobutylicum with RNA sequencing
The C. acetobutylicum genome annotation has been markedly improved by integrating bioinformatic predictions with RNA sequencing(RNA-seq) data. Samples were acquired under butanol, butyrate, and unstressed treatments across various growth stages to sample the transcriptome from a range of …
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Evolution of Protein Structure
… in homology detection searches, a key step in genome annotation, over the Swiss-Prot and NCBI non-redundant sequence databases.
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Studies of exon scrambling and mutually exclusive alternative splicing
… exons. Stringent criteria were used to exclude genome annotation or assembly artifacts. This search identified 172 human ESTs representing 90 exon scrambling events, which derive from 85 different human genes. In several cases, the scrambled transcripts were validated using an RT-PCR-sequencing …
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INSIGHTS INTO THE GENETIC DIVERSITY OF ASIMINA TRILOBA: A STUDY USING GENOME ASSEMBLY AND POPULATION GENETICS
… this, we have produced a high-quality reference genome by assembling a draft genome using PacBio's Sequel II long reads and polishing with Illumina short reads. We first used a genotype-by-sequencing (GBS) to genotype 124 individuals from 28 sites across the state of Virginia to produce a set of …
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Comprehensive analysis of high-throughput experiments for investigating transcription and transcriptional regulation
As the number of fully sequenced genomes grows, efforts are shifted towards investigation of functional aspects. One research focus is the transcriptome, the set of all transcribed genomic features. We aspire to understand what features constitute the transcriptome, in which context these are …
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Multi-omics Investigation into Alzheimer's Disease: Functional Mechanism and Early Detection
… integrative analysis of summary statistics from genome-wide association study (GWAS) and expression quantitative trait loci (eQTL) analysis. Results of this study confirmed the potential of integrative GWAS and eQTL analysis in estimating the transcriptomic changes when lack of tissue-specific …
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Key role and diversity of EcR/USP and other nuclear receptors in selected Arthropoda species
… Over the last few years, the number of genome sequencing projects that are carried out for Arthropoda is rapidly increasing. This gave us the opportunity to investigate the NRs in a number of other arthropods and compare the sets of NRs between some of these groups. We chose three …
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Computational Identification and Functional Characterisation of Candidate DNA Binding Effectors in <i>Phytophthora</i>
… cycle.<br/>We hypothesise that Phytophthora genomes encode effectors that translocate into host nuclei during infection, where they bind DNA and modify gene expression. Computational methods for predicting DNA-binding proteins can provide a high-throughput means of candidate selection. …
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The Energy Landscape of Associative Memory Energy Functions and Their Application to Ab Initio Protein Structure Prediction
… to be useful in such large scale applications as genome annotation.
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Whole Genome Analysis of Escherichia coli and Pseudomonas aeruginosa Mixed Culture Biofilms Grown for 117 Days in Spaceflight
… isolates were chosen to undergo whole genome sequencing to be compared to the ancestral strain genomes. Illumina and Nanopore reads were used obtain draft genomes via a hybrid assembly. Whole genome alignment was used to identify differences, including SNPs, amongst the spaceflight …
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Bioinformatics approaches to large scale genome comparison, including the identification of conserved noncoding regions
… much about the structure and organization of genomes. REPuter is a bioinformatics tool that efficiently finds repeatitive substrings in large genomic sequences. The identification of repeats enables a wide range of biological interpretations. Here we describe how this single software is …
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