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 12 of 12 for “"Genome Comparison"”.
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Typing and genome comparison of Neisseria meningitidis by DNA-microarrays
… strains and other ST-11 strains using whole genome microarray technology. Three genes encoding hypothetical proteins were identified to be present in all ET-15 strains but absent in other ST-11 strains. This finding together with unpublished observation from our group suggested that several …
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Algorithms for pre-microrna classification and a GPU program for whole genome comparison
… with pre-miRNA-like hairpin can be found in genomes. It is a challenge to distinguish the real pre-miRNAs from other hairpin sequences with similar stem-loops (referred to as pseudo pre-miRNAs). The first part of this dissertation presents a new method, called MirID, for identifying and …
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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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Comparative Genome Analysis of Three Brucella spp. and a Data Model for Automated Multiple Genome Comparison
Comparative analysis of multiple genomes presents many challenges ranging from management of information about thousands of local similarities to definition of features by combination of evidence from multiple analyses and experiments. This research represents the development stage of a …
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Comparative Analysis of Genomic Similarity Tools in Species Identification
… and evaluation of an automated pipeline for genome comparison, leveraging four bioinformatics tools: alignment-based methods (pyANI, Fas- tANI) and k-mer-based methods (Sourmash, BinDash 2.0). The analysis focuses on high- quality genomic datasets characterized by 100% completeness, ensuring …
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Exploring Genome Structure and Gene Regulation Related to Virulence in Fungal Phytopathogens Using Next Generation Sequencing Techniques
… Applications of NGS include studies of entire genomes, characterization of the entire transcriptome (RNA-Seq), and detection of protein-DNA binding sites (ChIP-Seq). The cost of sequencing a fungal genome, for example, has decreased from more than one hundred thousand dollars to currently only …
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Incorporation of Physico-Chemical Parameters Into Design of Microarray Experiments
… among the known Brucella species. A 3-way genome comparison identified a set of genes which occur uniquely in only one or two of the sequenced Brucella genomes. Reverse transcriptase PCR assays of over one hundred unique and pairwise-differential regions identified in Brucella revealed …
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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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Computational methods for genome screening
… encode. The development of new technologies for genome sequencing in the last years, opened new fundamental problems since huge amounts of biological data still deserve an interpretation. Indeed, the sequencing is only the first step of the genome annotation process that consists in the …
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Phenotypic and Genotypic Characteristics for Escherichia coli strains responsible for bacterial bloom events in Australia
… and capsule-negative strains. A pan genome comparison of phylogroup A E. coli revealed that the iron uptake system encoded by fecIRABCDE operon was over-represented among bloom strains (100%) compared to non-bloom E. coli (<39%). Growth assays however showed that the fec operon is …
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Phenotypic and Genotypic Characteristics for Escherichia coli strains responsible for bacterial bloom events in Australia
… and capsule-negative strains. A pan genome comparison of phylogroup A E. coli revealed that the iron uptake system encoded by fecIRABCDE operon was over-represented among bloom strains (100%) compared to non-bloom E. coli (<39%). Growth assays however showed that the fec operon is …
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Computational methods for the analysis of protein structure and function
… 5-10% of the protein sequences in the various genomes. Given their biological importance, in my work I introduced a Hidden Markov Model (HMM) that exploits the evolutionary information derived from multiple sequence alignments, to predict coiled-coil regions and to discriminate coiled-coil …