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Bradwell, Katie. "Genomic comparisons and genome architecture of divergent Trypanosoma species." VCU Scholars Compass, 2016. http://scholarscompass.vcu.edu/etd/4598.
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Virulent Trypanosoma cruzi, and the non-pathogenic Trypanosoma conorhini and Trypanosoma rangeli are protozoan parasites with divergent lifestyles. T. cruzi and T. rangeli are endemic to Latin America, whereas T. conorhini is tropicopolitan. Reduviid bug vectors spread these parasites to mammalian hosts, within which T. rangeli and T. conorhini replicate extracellularly, while T. cruzi has intracellular stages. Firstly, this work compares the genomes of these parasites to understand their differing phenotypes. Secondly, genome architecture of T. cruzi is examined to address the effect of a complex hybridization history, polycistronic transcription, and genome plasticity on this organism, and study its highly repetitive nature and cryptic genome organization. Whole genome sequencing, assembly and comparison, as well as chromosome-scale genome mapping were employed. This study presents the first comprehensive whole-genome maps of Trypanosoma, and the first T. conorhini strain ever sequenced. Original contributions vii to knowledge include the ~21-25 Mbp assembled genomes of the less virulent T. cruzi G, T. rangeli AM80, and T. conorhini 025E, containing ~10,000 to 13,000 genes, and the ~36 Mbp genome assembly of highly virulent T. cruzi CL with ~24,000 genes. The T. cruzi strains exhibited ~74% identity to proteins of T. rangeli or T. conorhini. T. rangeli and T. conorhini displayed greater complex carbohydrate metabolic capabilities, and contained fewer retrotransposons and multigene family copies, e.g. mucins, DGF-1, and MASP, compared to T. cruzi. Although all four genomes appear highly syntenic, T. rangeli and T. conorhini exhibited greater karyotype conservation. T. cruzi genome architecture studies revealed 66 maps varying from 0.13 to 2.4 Mbp. At least 2.6% of the genome comprises highly repetitive repeat regions, and 7.4% exhibits repetitive regions barren of labels. The 66 putative chromosomes identified are likely diploid. However, 20 of these maps contained regions of up to 1.25 Mbp of homology to at least one other map, suggestive of widespread segmental duplication or an ancient hybridization event that resulted in a genome with significant redundancy. Assembled genomes of these parasites closely reflect their phylogenetic relationships and give a greater context for understanding their divergent lifestyles. Genome mapping provides insight on the genomic evolution of these parasites.
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Li, Alice Hoy Lam. "Identification of virulence determinants of Mycobacterium tuberculosis via genetic comparisons of a virulent and an attenuated strain of Mycobacterium tuberculosis." Thesis, University of British Columbia, 2008. http://hdl.handle.net/2429/596.
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Candidate virulence genes were sought through the genetic analyses of two strains of Mycobacterium tuberculosis, one virulent, H37Rv, one attenuated, H37Ra. Derived from the same parent, H37, genomic differences between strains were first examined via two-dimensional DNA technologies: two-dimensional bacterial genome display, and bacterial comparative genomic hybridisation. The two-dimensional technologies were optimised for mycobacterial use, but failed to yield reproducible genomic differences between the two strains. Expression differences between strains during their infection of murine bone-marrow-derived macrophages were then assessed using Bacterial Artificial Chromosome Fingerprint Arrays. This technique successfully identified expression differences between intracellular M. tuberculosis H37Ra and H37Rv, and six candidate genes were confirmed via quantitative real-time PCR for their differential expression at 168 hours post-infection. Genes identified to be upregulated in the attenuated H37Ra were frdB, frdC, and frdD. Genes upregulated in the virulent H37Rv were pks2, aceE, and Rv1571. Further qPCR analysis of these genes at 4 and 96h post-infection revealed that the frd operon (encoding for the fumarate reductase enzyme complex or FRD) was expressed at higher levels in the virulent H37Rv at earlier time points while the expression of aceE and pks2 was higher in the virulent strain throughout the course of infection. Assessment of frd transcripts in oxygen-limited cultures of M. tuberculosis H37Ra and H37Rv showed that the attenuated strain displayed a lag in frdA and frdB expression at the onset of culture when compared to microaerophilic cultures of H37Rv and aerated cultures of H37Ra. Furthermore, inhibition of the fumarate reductase complex in intracellular bacteria resulted in a significant reduction of intracellular growth. Microarray technology was also applied in the expression analysis of intracellular bacteria at 168h post-infection. Forty-eight genes were revealed to be differentially expressed between the H37Ra and H37Rv strains, and a subset were further analysed via qPCR to confirm and validate the microarray data. phoP was expressed at a lower level in the attenuated M. tuberculosis H37Ra, whereas members of the phoPR regulon were up-regulated in the virulent H37Rv. Additionally, a group of genes (Rv3616c-Rv3613c) that may associate with the region of difference 1 were also up-regulated in the virulent H37Rv.
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Batzoglou, Serafim. "Computational genomics : mapping, comparison, and annotation of genomes." Thesis, Massachusetts Institute of Technology, 2000. http://hdl.handle.net/1721.1/8629.
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Thesis (Ph. D.)--Massachusetts Institute of Technology, Dept. of Electrical Engineering and Computer Science, 2000.Includes bibliographical references (leaves 180-191).
The field of genomics provides many challenges to computer scientists and mathematicians. The area of computational genomics has been expanding recently, and the timely application of computer science in this field is proving to be an essential component of the large international effort in genomics. In this thesis we address key issues in the different stages of genome research: planning of a genome sequencing project, obtaining and assembling sequence information, and ultimately study, cross-species comparison, and annotation of finished genomic sequence. We present applications of computational techniques to the above areas: (1) In relation to the early stages of a genome project, we address physical mapping, and we present results on the theoretical problem of finding minimum superstrings of hypergraphs, a combinatorial problem motivated by physical mapping. We also present a statistical and simulation study of "walking with clone-end sequences", an important method for sequencing a large genome.
(cont.) (2) Turning to the problem of obtaining the finished genomic sequence, we present ARACHNE, a prototype software system for assembling sequence data that are derived from sequencing a genome with the "shotgun" method. (3) Finally, we turn to the computational analysis of finished genomic sequence. We present GLASS, a software system for obtaining global pairwise alignments of orthologous finished sequences. We finally use GLASS to perform a comparative structure and sequence analysis of orthologous human and mouse genomic regions, and develop ROSETTA, the first cross-species comparison-based system for the prediction of protein coding regions in genomic sequences.
by Serafin Batzoglou.
Ph.D.
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Dousseaud, Peggy Marie Madeleine. "A comparative genomic analysis of hydrocarbon synthesis in Desulfovibrio sp." Thesis, University of Exeter, 2018. http://hdl.handle.net/10871/34379.
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To fulfil global energy demand and to mitigate economical, geopolitical and ecological challenges associated with fossil fuel utilisation, the energy sector is moving towards greater use of sustainable and environmentally friendly energy sources, including biofuels. The ideal transport biofuel would be hydrocarbons that are identical to fossil petroleum. However, to date characterised hydrocarbon biosynthetic pathways include a decarbonylation or decarboxylation reaction, which involves the loss of one carbon resulting in odd-numbered carbon chain hydrocarbons. This carbon loss decreases carbon efficiency for alkane production, which reduces microbial fuel economic competitiveness. Therefore, it is key that new pathways for alkane production are identified. The sulphate-reducing bacteria genus Desulfovibrio was previously reported to synthesise even-numbered carbon chain alkanes, which suggests an alternative route for alkane production without carbon loss. This investigation aimed to verify Desulfovibrio alkane biosynthesis and characterise the possible synthetic pathway. Ten Desulfovibrio strains, representing seven species, were screened for alkane synthesis using isotopically labelled growth media. The ability to produce alkanes within the Desulfovibrio genus was confirmed and was shown to be strain-specific under a set of culture conditions. The biogenic alkanes detected were octadecane (C18), nonadecane (C19) and eicosane (C20), with a predominance of even-numbered carbon chain alkanes. Fatty acid analysis of Desulfovibrio strains showed an alkane biosynthetic pathway was unlikely to involve a decarbonylation or decarboxylation step. A novel hypothesis was therefore proposed that alkane biosynthesis by Desulfovibrio follows a metabolic route, which has not previously been characterised, involving a series of reduction reactions from the fatty acid pool. The characterisation of the putative Desulfovibrio hydrogenation pathway for alkane biosynthesis was undertaken via a target-directed genome mining approach. The genomic DNA of nine Desulfovibrio spp. was purified, sequenced, de novo assembled and annotated. Seven of these nine genomes are unpublished to date. No homologs of previously characterised alkane biosynthetic enzymes from bacteria were in silico identified in the genomes and proteomes of alkane producing Desulfovibrio spp., suggesting that Desulfovibrio alkane biosynthetic pathway is likely to be catalysed by currently uncharacterised enzymes. The 16S rRNA-based phylogeny of Desulfovibrio spp. supported the hypothesis that the Desulfovibrio alkane biosynthetic pathway was acquired by a common ancestral strain via horizontal gene transfer. The ability of Desulfovibrio to produce alkanes was therefore hypothesised to be due to the presence of recruited genes encoding enzymes involved in alkane synthesis. A comparative genomic analysis intersecting six-alkane producing and four non-alkane producing Desulfovibrio genomes resulted in the in silico identification of 33 hypothetical proteins considered with high confidence to be exclusive to alkane producing Desulfovibrio strains. A novel hypothetical Desulfovibrio alkane biosynthetic pathway was proposed involving a V-type ATPase, an uncharacterised protein, named as a putative reductase in this investigation, and a putative methyltransferase, which were predicted to be exclusive to alkane producing Desulfovibrio spp. The inorganic phosphates resulting from the ATP hydrolysis catalysed by the V-type ATPase would be involved in a reaction with fatty alcohols to form alkyl phosphates, which are putative activated intermediates required for the hydrogenation route from fatty alcohols to alkanes. The putative reductase and the methyltransferase, predicted to share similar structural features with known alkane-binding proteins, would subsequently reduce alkyl phosphates to alkanes and to iso-alkanes respectively. Empirical investigation of the candidate molecular basis function in Desulfovibrio alkane biosynthesis was undertaken. The Desulfovibrio alkane biosynthetic pathway remains to be fully characterised.
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Jain, Gaurav. "Genomic comparison of species based on metabolic pathway components." Access to citation, abstract and download form provided by ProQuest Information and Learning Company; downloadable PDF file, 61 p, 2008. http://proquest.umi.com/pqdweb?did=1605156451&sid=3&Fmt=2&clientId=8331&RQT=309&VName=PQD.
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Thesis (M.S.)--University of Delaware, 2008.Principal faculty advisors: Li Liao, Dept. of Computer & Information Sciences and E. Fidelma Boyd, Dept. of Biological Sciences. Includes bibliographical references.
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Sharma, Ruchira. "Isolation, Characterization, and Genomic Comparison of Bacteriophages of Enterobacteriales Order." BYU ScholarsArchive, 2019. https://scholarsarchive.byu.edu/etd/8577.
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According to CDC, every year at least 2 million people are affected and 23,000 dies as a result of antibiotic resistance in U.S. It is considered one of the biggest threats to global health. More and more bacterial infections are becoming harder to treat. One such infection is fire blight, one of the most destructive disease of apple and pear trees. It is caused by bacteria Erwinia amylovora and its outbreaks have been known to destroy entire orchards in a single season. The conventional method of treatments includes use of antibiotics like streptomycin and oxytetracycline but the incidences like presence of multi-drug resistant bacteria in the mammals grazing in the fields have raised concerns. Phage therapy is considered one of the few ways available to combat bacterial resistance and prevent fire blight. In this method, a cocktail of highly lytic bacteriophages is prepared and sprayed on the trees at different time intervals. Bacteriophages are an “intelligent” drug. They multiply at the site of the infection until there are no more bacteria and then they are excreted back into the nature. These phenomena make them more efficient than an antibiotic, which kills all kind of bacteria including good bacteria and can be maintained in the environment for long periods of time. These qualities of bacteriophage have resulted in many commercially available phage therapies. The initial part of this research focuses on isolation, characterization and genomic comparison of bacteriophages that infect a plant pathogen E.amylovora of Erwiniaceae family of Enterobacteriales order. In this study, 28 novel bacteriophages were isolated, fully sequenced, characterized and grouped into seven families based on phage homology. To take this further, we characterized a novel jumbo family of bacteriophages that has a small burst size of 4.6-4.9 and are most similar to bacteriophages that infect Pseudomonas and Ralstonia rather than Enterobacteriales bacteria by protein similarity. These bacteriophages are shown to infect Erwinia and Pantoea bacterial strains, but no infection of 9 other bacterial strains tested, was seen, under laboratory conditions. The results of this work provide an insight on special characteristics that makes bacteriophage so unique and adaptable. The final part of this research explores the enormous diversity of bacteriophages. In 2014 Grose and Casjens grouped 337 fully sequenced tailed phages into 56 diverse clusters (32 lytic and 24 temperate). We further expanded our current understanding of these clusters by performing the comprehensive analysis of genomes and proteomes of 1037 tailed bacteriophages, posted on GenBank. The results of this work provide insights into diversity and relatedness of bacteriophages and the data is posted on GenBank.
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Dong, Xin. "Comparative genomics of rickettsia species." Thesis, Aix-Marseille, 2012. http://www.theses.fr/2012AIXM5054/document.
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Le genre Rickettsia, sont des petites bactéries Gram-négatives et symbiotes intracellulaires obligatoires des eucaryotes. Les Rickettsia sont surtout connus pour leur pathogénicité et pour provoquer des maladies graves chez l'homme et les autres animaux. À ce jour, 26 espèces valides de Rickettsies ont été identifiées dans le monde entier, dont 20 sont des agents pathogènes éprouvées. Toutes les espèces de Rickettsies validées sont associées à des arthropodes. Les phylogénies basées sur divers marqueurs moléculaires ont présenté des topologies discordantes, avec seulement R. bellii et R. canadensis qui ne sont classées ni parmi la fièvre boutonneuse groupe rickettsies, ni parmi le typhus groupe rickettsies. En utilisant les méthodes avancées de séquençage de génomes entiers, nous avons obtenu et analysé quatre séquences génomiques de Rickettsies : R. helvetica, R. honei, R. australis et R. japonica. Via la phylogénomique qui constitue une nouvelle stratégie permettant de mieux comprendre leur évolution, l'on remarque que ces micro-organismes ont subi une évolution génomique réduite au cours de spécialisation en intracellulaire. Plusieurs caractéristiques évolutives, comme le réarrangement des gènes, la réduction génomique, le transfert horizontal de gènes et l'acquisition d'ADN égoïste, ont formé les génomes Rickettsia d'aujourd'hui. Ces processus peuvent jouer un rôle important pour équilibrer la taille du génome afin de l'adapter au mode de vie intracellulaire. En outre, la pathogénicité des rickettsies peut être associée à la réduction génomiqueThe Rickettsia genus is composed of small, Gram-negative, bacteria that are obligate intracellular eukaryotic symbionts. Members of the genus Rickettsia are best known for infecting and causing severe diseases in humans and other animals. To date, 26 valid Rickettsia species have been identified worldwide, including 20 that are proven pathogens. All validated Rickettsia species are associated to arthropods that act as vectors and/or reservoirs. The phylogenies based on various molecular markers have resulted in discrepant topologies, with R. bellii and R. canadensis being classified neither among spotted fever nor typhus group rickettsiae. In this thesis, using the advanced whole genomic sequencing methods, we have and analyzed the genomic sequences from four Rickettsia species, including R. helvetica, R. honei, R. australis and R. japonica. Phylogenomics constitute a new strategy to better understand their evolution. These microorganisms underwent a reductive genomic evolution during their specialization to their intracellular lifestyle. Several evolutive characteristics, such as gene rearrangement, reduction, horizontal gene transfer and aquisition of selfish DNA, have shaped Rickettsia genomes. These processes may play an important role in free-living bacteria for balancing the size of genome in order to adapt the intracellular life style. In addition, in contrast with the concept of bacteria becoming pathogens by acquisition of virulence factors, rickettsial pathogenecity may be linked to genomic reduction of metabolism and regulation pathways
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Wetterbom, Anna. "Genome and Transcriptome Comparisons between Human and Chimpanzee." Doctoral thesis, Uppsala universitet, Genomik, 2010. http://urn.kb.se/resolve?urn=urn:nbn:se:uu:diva-112893.
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The chimpanzee is humankind’s closest living relative and the two species diverged ~6 million years ago. Comparative studies of the human and chimpanzee genomes and transcriptomes are of great interest to understand the molecular mechanisms of speciation and the development of species-specific traits. The aim of this thesis is to characterize differences between the two species with regard to their genome sequences and the resulting transcript profiles. The first two papers focus on indel divergence and in particular, indels causing premature termination codons (PTCs) in 8% of the chimpanzee genes. The density of PTC genes is correlated with both the distance to the telomere and the indel divergence. Many PTC genes have several associated transcripts and since not all are affected by the PTC we propose that PTCs may affect the pattern of expressed isoforms. In the third paper, we investigate the transcriptome divergence in cerebellum, heart and liver, using high-density exon arrays. The results show that gene expression differs more between tissues than between species. Approximately 15% of the genes are differentially expressed between species, and half of the genes show different splicing patterns. We identify 28 cassette exons which are only included in one of the species, often in a tissue-specific manner. In the fourth paper, we use massive parallel sequencing to study the chimpanzee transcriptome in frontal cortex and liver. We estimate gene expression and search for novel transcribed regions (TRs). The majority of TRs are located close to genes and possibly extend the annotations. A subset of TRs are not found in the human genome. The brain transcriptome differs substantially from that of the liver and we identify a subset of genes enriched with TRs in frontal cortex. In conclusion, this thesis provides evidence of extensive genomic and transcriptomic variability between human and chimpanzee. The findings provide a basis for further studies of the underlying differences affecting phenotypic divergence between human and chimpanzee.
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Dickens, Nicholas J. "Comparisons of proteins and genomes by integrating bioinformatics data." Thesis, University of Oxford, 2006. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.496848.
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Dörr, Daniel [Verfasser]. "Gene family-free genome comparison / Daniel Dörr." Bielefeld : Universitätsbibliothek Bielefeld, 2016. http://d-nb.info/1096457229/34.
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Mok, Kwai-lung. "Computational discovery of cis-regulatory modules in human genome by genome comparison." Click to view the E-thesis via HKUTO, 2008. http://sunzi.lib.hku.hk/hkuto/record/b40203621.
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Mok, Kwai-lung, and 莫貴龍. "Computational discovery of cis-regulatory modules in human genome by genome comparison." Thesis, The University of Hong Kong (Pokfulam, Hong Kong), 2008. http://hub.hku.hk/bib/B40203621.
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Bendezu, Angulo Ivan Fedor. "Comparison of genetic variability in European and South American populations of potato cyst nematodes measured by variation in DNA and virulence towards plant resistance genes." Thesis, University of Nottingham, 1997. https://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.363597.
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The genomic variability of sixty-nine populations of the potato cyst nematodes (PCN) Globodera pallida and G. rostochiensis from Europe and South America were analyzed using the RAPD-PCR technique with sixty-six 10-mer primers. Large genomic differences were found between the two PCN species (i.e. 33%). The genomic pool of British G. pallida populations showed considerably less variation than the Peruvian populations, with 73% and 41% similarity between populations respectively. The genomic similarity among populations of G. rostochiensis was 89% for UK populations and 82% when the two continental European populations were included. Nevertheless, between populations within each species and from the same locality, genomic differences were still found. The RAPD-PCR technique proved to be useful for revealing the genomic variability between and within species using DNA extracted from 50 cysts, but it gave variable results when DNA extracted from individual females or cysts was used, suggesting that for evaluating the genomic variability of individuals it is better to use specific primers. RAPD-PCR was also used successfully to distinguish the two PCN species, individuals selected and selected for virulence and even biotypes using individual cysts. Based on the results found when comparing biotypes of Globodera pallida, it is suggested that all the biotypes considered in the International Pathotype Scheme could be grouped into Pa1 and Pa2/3 when classifying European populations, and Pa1A or Pa1B, P4A, P5A and P6A when analyzing South American populations. However, these groupings should be regarded just as a reference, because virulence bioassay results plus the data found using the RAPD-PCR technique suggested that, at least in G. pallida, virulence seems to be a polygenic trait ruled by several genes with additive effects. On the other hand, based on the same sort of data, virulence in G. rostochiensis seems to be ruled only by major genes. Selected and unselected populations of G. pallida, reared on either potato clone Solanum vernei (VTn)2 62.33.3 or a susceptible control, were distinguished using the RAPD-PCR technique and primers Operon A-07, E-06, G-16 and I-05. Three of the fragments that appeared to distinguish the unselected from the selected populations were cloned into an isolate of E. coli and their sequences obtained. Gpalpha, seems to be part of a promoter region of a gene probably related or linked to virulence. The use of differential clones to characterize PCN populations with different proportions of each virulence gene is a valuable tool. Whilst diagnostic probes for routine identification of virulent populations are being developed, the use of the “gene pool similarities” concept involving the DNA patterns of standard populations as genetic virulence types (i.e. virulence biotypes), integrated with information on their response to differential clones bearing genes for resistance, would represent the best approach towards devising a sustainable control strategy to optimize the usefulness of whatever resistance is available.
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Mitchell, Candice Melissa. "Morphologic and genomic characterisation of the koala Chlamydia pneumoniae strain." Thesis, Queensland University of Technology, 2010. https://eprints.qut.edu.au/33259/1/Candice_Mitchell_Thesis.pdf.
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Chlamydia pneumoniae is a common human and animal pathogen associated with a wide range of upper and lower respiratory tract infections. In more recent years there has been increasing evidence to suggest a link between C. pneumoniae and chronic diseases in humans, including atherosclerosis, stroke and Alzheimer’s disease. C. pneumoniae human strains show little genetic variation, indicating that the human-derived strain originated from a common ancestor in the recent past. Despite extensive information on the genetics and morphology processes of the human strain, knowledge concerning many other hosts (including marsupials, amphibians, reptiles and equines) remains virtually unexplored. The koala (Phascolarctos cinereus) is a native Australian marsupial under threat due to habitat loss, predation and disease. Koalas are very susceptible to chlamydial infections, most commonly affecting the conjunctiva, urogenital tract and/or respiratory tract. To address this gap in the literature, the present study (i) provides a detailed description of the morphologic and genomic architecture of the C. pneumoniae koala (and human) strain, and shows that the koala strain is microscopically, developmentally and genetically distinct from the C. pneumoniae human strain, and (ii) examines the genetic relationship of geographically diverse C. pneumoniae isolates from human, marsupial, amphibian, reptilian and equine hosts, and identifies two distinct lineages that have arisen from animal-to-human cross species transmissions. Chapter One of this thesis explores the scientific problem and aims of this study, while Chapter Two provides a detailed literature review of the background in this field of work. Chapter Three, the first results chapter, describes the morphology and developmental stages of C. pneumoniae koala isolate LPCoLN, as revealed by fluorescence and transmission electron microscopy. The profile of this isolate, when cultured in HEp-2 human epithelial cells, was quite different to the human AR39 isolate. Koala LPCoLN inclusions were larger; the elementary bodies did not have the characteristic pear-shaped appearance, and the developmental cycle was completed within a shorter period of time (as confirmed by quantitative real-time PCR). These in vitro findings might reflect biological differences between koala LPCoLN and human AR39 in vivo. Chapter Four describes the complete genome sequence of the koala respiratory pathogen, C. pneumoniae LPCoLN. This is the first animal isolate of C. pneumoniae to be fully-sequenced. The genome sequence provides new insights into genomic ‘plasticity’ (organisation), evolution and biology of koala LPCoLN, relative to four complete C. pneumoniae human genomes (AR39, CWL029, J138 and TW183). Koala LPCoLN contains a plasmid that is not shared with any of the human isolates, there is evidence of gene loss in nucleotide salvage pathways, and there are 10 hot spot genomic regions of variation that were previously not identified in the C. pneumoniae human genomes. Sequence (partial-length) from a second, independent, wild koala isolate (EBB) at several gene loci confirmed that the koala LPCoLN isolate was representative of a koala C. pneumoniae strain. The combined sequence data provides evidence that the C. pneumoniae animal (koala LPCoLN) genome is ancestral to the C. pneumoniae human genomes and that human infections may have originated from zoonotic infections. Chapter Five examines key genome components of the five C. pneumoniae genomes in more detail. This analysis reveals genomic features that are shared by and/or contribute to the broad ecological adaptability and evolution of C. pneumoniae. This analysis resulted in the identification of 65 gene sequences for further analysis of intraspecific variation, and revealed some interesting differences, including fragmentation, truncation and gene decay (loss of redundant ancestral traits). This study provides valuable insights into metabolic diversity, adaptation and evolution of C. pneumoniae. Chapter Six utilises a subset of 23 target genes identified from the previous genomic comparisons and makes a significant contribution to our understanding of genetic variability among C. pneumoniae human (11) and animal (6 amphibian, 5 reptilian, 1 equine and 7 marsupial hosts) isolates. It has been shown that the animal isolates are genetically diverse, unlike the human isolates that are virtually clonal. More convincing evidence that C. pneumoniae originated in animals and recently (in the last few hundred thousand years) crossed host species to infect humans is provided in this study. It is proposed that two animal-to-human cross species events have occurred in the context of the results, one evident by the nearly clonal human genotype circulating in the world today, and the other by a more animal-like genotype apparent in Indigenous Australians. Taken together, these data indicate that the C. pneumoniae koala LPCoLN isolate has morphologic and genomic characteristics that are distinct from the human isolates. These differences may affect the survival and activity of the C. pneumoniae koala pathogen in its natural host, in vivo. This study, by utilising the genetic diversity of C. pneumoniae, identified new genetic markers for distinguishing human and animal isolates. However, not all C. pneumoniae isolates were genetically diverse; in fact, several isolates were highly conserved, if not identical in sequence (i.e. Australian marsupials) emphasising that at some stage in the evolution of this pathogen, there has been an adaptation/s to a particular host, providing some stability in the genome. The outcomes of this study by experimental and bioinformatic approaches have significantly enhanced our knowledge of the biology of this pathogen and will advance opportunities for the investigation of novel vaccine targets, antimicrobial therapy, or blocking of pathogenic pathways.
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Zerbino, Daniel Robert. "Genome assembly and comparison using de Bruijn graphs." Thesis, University of Cambridge, 2009. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.611752.
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Vorster, Barend Juan. "Using whole genome comparison to detect sequence similarities between plants and microbes." Electronic thesis, 2007. http://upetd.up.ac.za/thesis/available/etd-01192009-142048.
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Puterová, Janka. "Porovnání eukaryotních genomů." Master's thesis, Vysoké učení technické v Brně. Fakulta informačních technologií, 2015. http://www.nusl.cz/ntk/nusl-264943.
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Main motive of this master thesis was the need of good bioinformatics tools for genome comparison and improvement of one of the existing tools - RepeatExplorer. This work offers an overview of transposable elements in DNA, existing tools for identification and analysis of repetitions in sequenced genomes, summary of currently used genome sequencing methods. This work describes shortcomings of RepeatExplorer tool with focus on comparative analysis of genomes. Two solutions to remove these problems were designed and implemented. The first solution is designed for comparing pairs of genomes. The principle of this solution is based on comparison of similarity of distribution of contigs coverages using Kolmogorov-Smirnov test, thanks to which we are able to determine different parts in the genomes.The second solution, which is used to compare multiple genomes, is based on the method of mapping reads from compared genomes to the reference genome contigs and provides contigs coverage graphs, by which we are able to determine the variability of the repeats.Their functionality was verified on real NGS data of organism Silene latifolia.
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Novotny, Marian. "Applications of Structural Bioinformatics for the Structural Genomics Era." Doctoral thesis, Uppsala : Acta Universitatis Upsaliensis Acta Universitatis Upsaliensis, 2007. http://urn.kb.se/resolve?urn=urn:nbn:se:uu:diva-7593.
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Tang, Haibao, Eric Lyons, Brent Pedersen, James Schnable, Andrew Paterson, and Michael Freeling. "Screening synteny blocks in pairwise genome comparisons through integer programming." BioMed Central, 2011. http://hdl.handle.net/10150/610221.
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BACKGROUND:It is difficult to accurately interpret chromosomal correspondences such as true orthology and paralogy due to significant divergence of genomes from a common ancestor. Analyses are particularly problematic among lineages that have repeatedly experienced whole genome duplication (WGD) events. To compare multiple "subgenomes" derived from genome duplications, we need to relax the traditional requirements of "one-to-one" syntenic matchings of genomic regions in order to reflect "one-to-many" or more generally "many-to-many" matchings. However this relaxation may result in the identification of synteny blocks that are derived from ancient shared WGDs that are not of interest. For many downstream analyses, we need to eliminate weak, low scoring alignments from pairwise genome comparisons. Our goal is to objectively select subset of synteny blocks whose total scores are maximized while respecting the duplication history of the genomes in comparison. We call this "quota-based" screening of synteny blocks in order to appropriately fill a quota of syntenic relationships within one genome or between two genomes having WGD events.RESULTS:We have formulated the synteny block screening as an optimization problem known as "Binary Integer Programming" (BIP), which is solved using existing linear programming solvers. The computer program QUOTA-ALIGN performs this task by creating a clear objective function that maximizes the compatible set of synteny blocks under given constraints on overlaps and depths (corresponding to the duplication history in respective genomes). Such a procedure is useful for any pairwise synteny alignments, but is most useful in lineages affected by multiple WGDs, like plants or fish lineages. For example, there should be a 1:2 ploidy relationship between genome A and B if genome B had an independent WGD subsequent to the divergence of the two genomes. We show through simulations and real examples using plant genomes in the rosid superorder that the quota-based screening can eliminate ambiguous synteny blocks and focus on specific genomic evolutionary events, like the divergence of lineages (in cross-species comparisons) and the most recent WGD (in self comparisons).CONCLUSIONS:The QUOTA-ALIGN algorithm screens a set of synteny blocks to retain only those compatible with a user specified ploidy relationship between two genomes. These blocks, in turn, may be used for additional downstream analyses such as identifying true orthologous regions in interspecific comparisons. There are two major contributions of QUOTA-ALIGN: 1) reducing the block screening task to a BIP problem, which is novel2) providing an efficient software pipeline starting from all-against-all BLAST to the screened synteny blocks with dot plot visualizations. Python codes and full documentations are publicly available http://github.com/tanghaibao/quota-alignment webcite. QUOTA-ALIGN program is also integrated as a major component in SynMap http://genomevolution.com/CoGe/SynMap.pl webcite, offering easier access to thousands of genomes for non-programmers.
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Jaša, Petr. "Techniky pro získávání dat v genomice." Master's thesis, Vysoké učení technické v Brně. Fakulta informačních technologií, 2007. http://www.nusl.cz/ntk/nusl-412789.
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First of all, this thesis sets itself a goal to introduce some common technics for datamining in genomics and as a next step to implement own algorithm like algorithm BLAST. In the concrete, this work is pointed to sequences of DNA. The DNA sequence contains in itself genetic information, which is template for living organism. For explanation this information can be used number of technics. This paper describes algorithm Fasta and algorithms from BLAST family. With these algorithms, it is possible to gain a lot of important information even about such DNA sequences, where only primary structure is known. Principle of these algorithms is based on alignments of one query sequence, which we want to obtain some information from, with many sequences stored in database. According to result alignment, it is possible to determine many features of the query sequence.
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Peng, Liang. "Neighborhood-Oriented feature selection and classification of Duke’s stages on colorectal Cancer using high density genomic data." Kansas State University, 2011. http://hdl.handle.net/2097/10751.
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Master of ScienceDepartment of Statistics
Haiyan Wang
The selection of relevant genes for classification of phenotypes for diseases with gene expression data have been extensively studied. Previously, most relevant gene selection was conducted on individual gene with limited sample size. Modern technology makes it possible to obtain microarray data with higher resolution of the chromosomes. Considering gene sets on an entire block of a chromosome rather than individual gene could help to reveal important connection of relevant genes with the disease phenotypes. In this report, we consider feature selection and classification while taking into account of the spatial location of probe sets in classification of Duke’s stages B and C using DNA copy number data or gene expression data from colorectal cancers. A novel method was presented for feature selection in this report. A chromosome was first partitioned into blocks after the probe sets were aligned along their chromosome locations. Then a test of interaction between Duke’s stage and probe sets was conducted on each block of probe sets to select significant blocks. For each significant block, a new multiple comparison procedure was carried out to identify truly relevant probe sets while preserving the neighborhood location information of the probe sets. Support Vector Machine (SVM) and K-Nearest Neighbor (KNN) classification using the selected final probe sets was conducted for all samples. Leave-One-Out Cross Validation (LOOCV) estimate of accuracy is reported as an evaluation of selected features. We applied the method on two large data sets, each containing more than 50,000 features. Excellent classification accuracy was achieved by the proposed procedure along with SVM or KNN for both data sets even though classification of prognosis stages (Duke’s stages B and C) is much more difficult than that for the normal or tumor types.
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Ong, Wai, Trang Vu, Klaus Lovendahl, Jenna Llull, Margrethe Serres, Margaret Romine, and Jennifer Reed. "Comparisons of Shewanella strains based on genome annotations, modeling, and experiments." BioMed Central, 2014. http://hdl.handle.net/10150/610105.
Full textAbstract:
BACKGROUND:Shewanella is a genus of facultatively anaerobic, Gram-negative bacteria that have highly adaptable metabolism which allows them to thrive in diverse environments. This quality makes them an attractive bacterial target for research in bioremediation and microbial fuel cell applications. Constraint-based modeling is a useful tool for helping researchers gain insights into the metabolic capabilities of these bacteria. However, Shewanella oneidensis MR-1 is the only strain with a genome-scale metabolic model constructed out of 21 sequenced Shewanella strains.RESULTS:In this work, we updated the model for Shewanella oneidensis MR-1 and constructed metabolic models for three other strains, namely Shewanella sp. MR-4, Shewanella sp. W3-18-1, and Shewanella denitrificans OS217 which span the genus based on the number of genes lost in comparison to MR-1. We also constructed a Shewanella core model that contains the genes shared by all 21 sequenced strains and a few non-conserved genes associated with essential reactions. Model comparisons between the five constructed models were done at two levels - for wildtype strains under different growth conditions and for knockout mutants under the same growth condition. In the first level, growth/no-growth phenotypes were predicted by the models on various carbon sources and electron acceptors. Cluster analysis of these results revealed that the MR-1 model is most similar to the W3-18-1 model, followed by the MR-4 and OS217 models when considering predicted growth phenotypes. However, a cluster analysis done based on metabolic gene content revealed that the MR-4 and W3-18-1 models are the most similar, with the MR-1 and OS217 models being more distinct from these latter two strains. As a second level of comparison, we identified differences in reaction and gene content which give rise to different functional predictions of single and double gene knockout mutants using Comparison of Networks by Gene Alignment (CONGA). Here, we showed how CONGA can be used to find biomass, metabolic, and genetic differences between models.CONCLUSIONS:We developed four strain-specific models and a general core model that can be used to do various in silico studies of Shewanella metabolism. The developed models provide a platform for a systematic investigation of Shewanella metabolism to aid researchers using Shewanella in various biotechnology applications.
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Tvedte, Eric S. "Genome evolution in parasitic wasps: comparisons of sexual and asexual species." Diss., University of Iowa, 2018. https://ir.uiowa.edu/etd/6516.
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The fate of any lineage is contingent on the rate at which its genome changes over time. Genome dynamics are influenced by patterns of mutation and recombination. Mutations as the raw force of variation can be acted on independently during exchanges of homologous genetic regions via meiotic recombination. While molecular evolution in sexual lineages is impacted by both mutation and recombination, asexual lineage fate is primarily influenced by the mutation rate; recombination is often altered or absent in asexuals. Although multiple studies show accelerated mutation accumulation in asexual lineages that have lost recombination, virtually nothing is known about rate patterns when meiosis is retained. Here, I use parasitic wasps in genus Diachasma to investigate genome evolution in a recently-derived asexual lineage. I provide evidence that asexual Diachasma possess a canonical set of meiosis genes as well as high levels of genomic homozygosity. Taken together, these observations support an active, albeit modified, form of meiosis in this asexual lineage. In addition, I present the first documentation of accelerated mutation accumulation in the nuclear genome of a naturally-occurring, meiotically- reproducing organism. If harmful, these mutations could impede asexual lineage persistence and contribute strong support for the long-term benefits of sex.
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Barbee, Bonnie. "Genomic Heterogeneity of Glioblastoma: A Comparison of the Enhancing Tumor Core and the Brain Around the Tumor." Thesis, The University of Arizona, 2016. http://hdl.handle.net/10150/603560.
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Older, Aguilar Anastazia Magdalena. "Comparison of genomic structure and MHC specificities of killer cell immunoglobulin-like receptors in humans and orangutans /." May be available electronically:, 2009. http://proquest.umi.com/login?COPT=REJTPTU1MTUmSU5UPTAmVkVSPTI=&clientId=12498.
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Wang, Hao. "THE POTENTIAL INDUCING PATTERN OF THE FLAX GENOME." Case Western Reserve University School of Graduate Studies / OhioLINK, 2019. http://rave.ohiolink.edu/etdc/view?acc_num=case1532609009820723.
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Kastenmüller, Gabriele. "In silico prediction and comparison of metabolic capabilities in sequenced genomes /." München : Hut, 2009. http://bvbr.bib-bvb.de:8991/F?func=service&doc_library=BVB01&doc_number=018929163&line_number=0001&func_code=DB_RECORDS&service_type=MEDIA.
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Sturgill, David Matthew. "Comparative Genome Analysis of Three Brucella spp. and a Data Model for Automated Multiple Genome Comparison." Thesis, Virginia Tech, 2003. http://hdl.handle.net/10919/10163.
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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 database-backed pipeline for comparative analysis of multiple genomes. The genomes of three recently sequenced species of Brucella were compared and a superset of known and hypothetical coding sequences was identified to be used in design of a discriminatory genomic cDNA array for comparative functional genomics experiments. Comparisons were made of coding regions from the public, annotated sequence of B. melitensis (GenBank) to the annotated sequence of B. suis (TIGR) and to the newly-sequenced B. abortus (personal communication, S. Halling, National Animal Disease Center, USDA).
A systematic approach to analysis of multiple genome sequences is described including a data model for storage of defined features is presented along with necessary descriptive information such as input parameters and scores from the methods used to define features. A collection of adjacency relationships between features is also stored, creating a unified database that can be mined for patterns of features which repeat among or within genomes.
The biological utility of the data model was demonstrated by a detailed analysis of the multiple genome comparison used to create the sample data set. This examination of genetic differences between three Brucella species with different virulence patterns and host preferences enabled investigation of the genomic basis of virulence. In the B. suis genome, seventy-one differentiating genes were found, including a contiguous 17.6 kb region unique to the species. Although only one unique species-specific gene was identified in the B. melitensis genome and none in the B. abortus genome, seventy-nine differentiating genes were found to be present in only two of the three Brucella species. These differentiating features may be significant in explaining differences in virulence or host specificity. RT-PCR analysis was performed to determine whether these genes are transcribed in vitro. Detailed comparisons were performed on a putative B. suis pathogenicity island (PAI). An overview of these genomic differences and discussion of their significance in the context of host preference and virulence is presented.Master of Science
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Santos, Almeida Alexandre Miguel. "Evolutionary insights into the host--specific adaptation and pathogenesis of group B Streptococcus Persistence of a dominant bovine lineage of group B Streptococcus reveals genomic signatures of host adaptation Whole-Genome Comparison Uncovers Genomic Mutations between Group B Streptococci Sampled from Infected Newborns and Their Mothers." Thesis, Paris 6, 2017. http://www.theses.fr/2017PA066029/document.
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Streptococcus agalactiae (streptocoque du groupe B, SGB) est un commensal fréquent des voies intestinale et génito-urinaire dans la population humaine mais constitue une des causes principales d'infections néonatales. Dans le même temps, SGB est connu comme pathogène vétérinaire, responsable de mastites bovines à l'origine de pertes économiques importantes dans plusieurs pays comme le Portugal. L'objectif de ma thèse était d'analyser au niveau génomique les bases de l'adaptation spécifique de SGB à ses hôtes humains et bovins et de l'établissement des lignées plus pathogènes. La comparaison des profils génomiques des souches isolées de nouveau-nés infectés et de leurs mères nous a permis de montrer que la transmission de SGB de mère à enfant est accompagnée dans certains cas par l'acquisition de mutations pathoadaptives. Par ailleurs, l'analyse des séquences génomiques de plus de 600 souches appartenant au complexe clonal (CC) 17, hypervirulent et spécifique à l'hôté humain, nous a permis de caractériser les forces évolutives agissant sur ce complexe. Finalement, l'étude de la colonisation des fermes laitières portugaises par un seul clone CC61 depuis plus de 20 ans a mis en évidence que la régulation spécifique de l'import du fer/manganèse est une stratégie d'adaptation récurrente dans l’environnement bovin. En conclusion, les résultats que nous présentons améliorent notre compréhension de l'adaptation chez les espèces hôte-généralistes, en apportant des idées utiles qui pourront spécifiquement aider à améliorer le contrôle et le traitement des infections de SGB mondialementStreptococcus agalactiae (group B Streptococcus, GBS) is a commensal of the intestinal and genitourinary tracts in the human population, while also a leading cause of neonatal infections. Likewise, GBS remains a serious concern in many countries as frequently responsible for bovine mastitis. Therefore, the purpose of my PhD project was to use state-of-the-art whole-genome approaches to decipher the host-specific adaptation and pathogenesis of GBS in both humans and bovines. By comparing the genomic profile of strains from infected newborns and their mothers we showed that the transmission of GBS from mother to child is accompanied in particular instances by the acquisition of specific pathoadaptive mutations. Moreover, from the study of the evolutionary forces acting on the human-specific and hypervirulent clonal complex (CC) 17, we reveal that various systems can evolve to improve the ability of GBS to survive in the human host. Functions related to metabolism, cell adhesion, regulation and immune evasion were among the most preferentially affected in GBS strains from human origin. Conversely, colonization of Portuguese dairy farms by one single CC61 clone for over 20 years highlighted that the specific regulation of iron/manganese uptake is a recurrent adaptive strategy in the bovine environment
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Nelson, Andrew D. L., Upendra K. Devisetty, Kyle Palos, Asher K. Haug-Baltzell, Eric Lyons, and Mark A. Beilstein. "Evolinc: A Tool for the Identification and Evolutionary Comparison of Long Intergenic Non-coding RNAs." FRONTIERS MEDIA SA, 2017. http://hdl.handle.net/10150/624658.
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Long intergenic non-coding RNAs (lincRNAs) are an abundant and functionally diverse class of eukaryotic transcripts. Reported lincRNA repertoires in mammals vary, but are commonly in the thousands to tens of thousands of transcripts, covering similar to 90% of the genome. In addition to elucidating function, there is particular interest in understanding the origin and evolution of lincRNAs. Aside from mammals, lincRNA populations have been sparsely sampled, precluding evolutionary analyses focused on their emergence and persistence. Here we present Evolinc, a two-module pipeline designed to facilitate lincRNA discovery and characterize aspects of lincRNA evolution. The first module (Evolinc-I) is a lincRNA identification workflow that also facilitates downstream differential expression analysis and genome browser visualization of identified lincRNAs. The second module (Evolinc-II) is a genomic and transcriptomic comparative analysis workflow that determines the phylogenetic depth to which a lincRNA locus is conserved within a user-defined group of related species. Here we validate lincRNA catalogs generated with Evolinc-I against previously annotated Arabidopsis and human lincRNA data. Evolinc-I recapitulated earlier findings and uncovered an additional 70 Arabidopsis and 43 human lincRNAs. We demonstrate the usefulness of Evolinc-II by examining the evolutionary histories of a public dataset of 5,361 Arabidopsis lincRNAs. We used Evolinc-II to winnow this dataset to 40 lincRNAs conserved across species in Brassicaceae. Finally, we show how Evolinc-II can be used to recover the evolutionary history of a known lincRNA, the human telomerase RNA (TERC). These latter analyses revealed unexpected duplication events as well as the loss and subsequent acquisition of a novel TERC locus in the lineage leading to mice and rats. The Evolinc pipeline is currently integrated in CyVerse's Discovery Environment and is free for use by researchers.
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Xue, Jianli. "Comparison of ascovirus and baculovirus genomes and their replication and gene expression strategies." Miami University / OhioLINK, 2011. http://rave.ohiolink.edu/etdc/view?acc_num=miami1312568903.
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Johnson, Carlena. "AXOLOTL PAEDOMORPHOSIS: A COMPARISON OF JUVENILE, METAMORPHIC, AND PAEDOMORPHIC AMBYSTOMA MEXICANUM BRAIN GENE TRANSCRIPTION." UKnowledge, 2013. http://uknowledge.uky.edu/biology_etds/13.
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Unlike many amphibians, the paedomorphic axolotl (Ambystoma mexicanum) rarely undergoes external morphological changes indicative of metamorphosis. However, internally, some axolotl tissues undergo cryptic metamorphic changes. A previous study examined interspecific patterns of larval brain gene expression and found that these species exhibited unique temporal expression patterns that were hypothesized to be morph specific. This thesis tested this hypothesis by examining differences in brain gene expression between juvenile (JUV), paedomorphic (PAED), and metamorphic (MET) axolotls. I identified 828 genes that were expressed differently between JUV, PAED, and MET. Expression estimates from JUV were compared to estimates from PAED and MET brains to identify genes that changed significantly during development. Genes that showed statistically equivalent expression changes across MET and PAED brains provide a glimpse at aging and maturation in an amphibian. The genes that showed statistically different expression estimates between metamorphic and paedomorphic brains provide new functional insights into the maintenance and regulation of paedomorphosis. For genes that were not commonly regulated due to aging, paedomorphs exhibited greater transcriptional similarity to juvenile than metamorphs did to juvenile. Overall, gene expression differences between metamorphic and paedomorphic development exhibit a mosaic pattern of expression as a function of aging and metamorphosis in axolotls.
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Choudhuri, Jomuna Veronica. "Bioinformatics approaches to large scale genome comparison, including the identification of conserved noncoding regions." [S.l. : s.n.], 2003. http://deposit.ddb.de/cgi-bin/dokserv?idn=968573630.
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Chen, Daidi. "Genetic studies on pleiotropic polyoxin resistant mutants of Bipolaris maydis." Kyoto University, 2018. http://hdl.handle.net/2433/232359.
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Kyoto University (京都大学)0048
新制・課程博士
博士(農学)
甲第21158号
農博第2284号
新制||農||1060(附属図書館)
学位論文||H30||N5132(農学部図書室)
京都大学大学院農学研究科地域環境科学専攻
(主査)教授 田中 千尋, 教授 本田 与一, 教授 宮川 恒
学位規則第4条第1項該当
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Garg, Kavita. "Genome-wide comparison of evolutionarily conserved alternative and constitutive splice sites /." Thesis, Connect to this title online; UW restricted, 2006. http://hdl.handle.net/1773/10260.
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Rasmussen, Samantha. "Predicting feed efficiency in beef cattle; a comparison of direct measures, expected progeny differences, and single nucleotide polymorphism methodologies." OpenSIUC, 2020. https://opensiuc.lib.siu.edu/theses/2685.
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Single nucleotide polymorphism (SNP) methodology is being used as a means to determine genetic merit in beef cattle by interrogating animal genomes and associating the findings with performance traits. The ability to predict future trait performance is highly attractive to beef cattle producers as they can make important management and financial decisions earlier and with more certainty. To fully realize the potential of SNP testing technology the methodology must be vetted to assure producer confidence. The purpose of this project is to assess three sources of information for beef cattle trait assessment. These information sources are: SNP testing, Expected Progeny Differences (EPDs) and direct animal measures. To conduct this study, young beef bulls (n=181) consigned to the SIU Beef Evaluation Station were utilized in an 84-day period to obtain direct measures. The SIU Beef Evaluation Station uses the Calan-Broadbent confinement feeding system which allows researchers to monitor individual animal feed intake and weight gain. Feed efficiency traits are important to the cattle industry since feed is generally among the largest input cost to producers. The evaluation of bulls also assesses reproductive and carcass traits which are also important to the producer’s financial success.Individual animal performance information was sent to the bull’s respective breed association for determination of EPD’s. Blood samples were submitted to a commercial company for SNP testing (Igentiy Gold and Igenity Beef Profile, Neogen, Lincoln, NE). Data was analyzed using pairwise comparisons by source of information. Pearson correlations were used to determine the direction and the strength for sources of information to vary together. Data was determined to be correlated when the correlation coefficient was 0.3 < r < - 0.3. No correlation was observed between RFISIU :RFINEO (r = 0.042), RFINEO:F/GSIU (r = - 0.09), RFISIU:ADGNEO (r = 0.091), RFISIU:ADGSIU (r = - 0.039), RFINEO:ADGNEO (r = 0.236), BWNEO:BWSIU (r = 0.115), FRAMESIU:BWSIU (r = 0.111), FRAMESIU:BWEPD (r = 0.159), FRAMESIU:ADGSIU (r = 0.148), FRAMESIU:ADGNEO (r = -0.005), BWSIU:BWEPD (r = 0.256), and BWNEO:BWEPD (r = 0.226). Correlations were observed between RFISIU:F/GSIU (r = 0.455), ADGSIU :ADGNEO (r = 0.353), and FRAMESIU:BWNEO (r = 0.326).This study determined that beef bulls should continue to be performance tested due to discrepancies between sources of information for key animal performance traits. Assessment of SNPs used in the commercial test should continue.
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Hultman, Cecilia. "Diatom and Cyanobacterial Symbioses : Identifying Environmental MAGs by Comparisons with Known Symbiotic Draft Genomes." Thesis, Umeå universitet, Institutionen för ekologi, miljö och geovetenskap, 2021. http://urn.kb.se/resolve?urn=urn:nbn:se:umu:diva-183999.
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The partnerships, or symbioses, between diatom hosts and cyanobacteria are widespread in the tropical and subtropical oceans. Many populate low nutrient waters where the heterocystous cyanobacteria fix N2 and provide reduced nitrogen (N) to the host. These types of symbioses are believed to be important in the global ocean biogeochemical cycle of N and carbon (C). The cyanobacteria morphology, cellular locations differ as well as genome size and content. The genome size and content are related to the cellular location: internal symbionts have smaller more eroded genomes, while external symbionts have larger genomes more similar to free-living cyanobacteria. Based on previously identified characteristics the aim of this report is to classify taxonomically, unidentified environmental metagenomic assembled genomes (MAGs) to the heterocystous symbionts of diatoms: Richelia and Calothrix. A select number of targeted gene sequences will be compared. MAGs and four draft genomes of Richelia and Calothrix were collected from public repositories (GTDB, NCBI and Tara project) and an initial comparison of GC-content and genome size was made. Based on this comparison, seven of the MAGs were determined as similar as the draft genomes of the known symbionts. After, a heatmap was created based on 27 targeted genes, some of which are highly conserved, to further characterize the phylogeny of the MAGs (Appendix 2). Results from the GC-content and genome size graph and the heatmap indicated similar trends which could connect one of the MAGs being most similar to the RintRC01 draft genome whereas the other five MAGs resembled the RintHH01 draft genome. Based on these results, conclusions can be drawn that the unknown MAGs are likely derived from symbionts of diatoms and could also possess similar characteristics, such as their cellular location, function and role in the N and C cycles.
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Bennett, Helen Victoria. "Giardia lamblia : a genome comparison of three reference strains using microarray technology." Thesis, Royal Holloway, University of London, 2010. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.538294.
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De, Maayer Pieter. "Genome comparisons to identify selected pathogenicity factors of a plant-associated Pantoea ananatis strain." Thesis, University of Pretoria, 2010. http://hdl.handle.net/2263/30849.
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Pantoea ananatis is a ubiquitous organism found in almost every environment on
earth. It has been implicated in diseases of a wide range of agronomic crops
worldwide, including onion, maize, rice and pineapple, as well as a human disease. In
South Africa, P. ananatis causes blight and dieback of Eucalyptus, resulting in severe
losses of this important forestry resource. Nevertheless, little is known about the
pathogenicity mechanisms utilised by this pathogen to cause disease in this host.
The whole genome of a highly virulent Eucalyptus-pathogenic P. ananatis strain,
LMG20103, was sequenced. This genome sequence was subsequently mined to
identify a vast array of genes encoding putative pathogenicity determinants.
Comparative genomics revealed that it has evolved to be able to thrive in a wide range
of environments and that this strain carries pathogenicity determinants that may allow
it to infect hosts in both the animal and plant Kingdom. Interestingly, no Type II and
III secretion systems, which form a major part of the pathogenicity arsenal of many
plant pathogenic bacteria are present in P. ananatis. However, three loci on the
genome encode three distinct copies of the Type VI secretion system, which has
recently been demonstrated to play an important role in diseases caused by many
plant- and animal-pathogenic bacteria. In silico analysis of these secretion systems
showed that they likely secrete several pathogenicity effectors which may have a role
in P. ananatis infection of both plant and animal hosts. Another putative
pathogenicity determinant identified from the genome, the exopolysaccharide
ananatan, was experimentally demonstrated to play a role in disease expression on
both onion seedlings and pineapple fruit. This was done through the production of a
library of mutants which encompasses all the genes on the P. ananatis genome.
Genome sequencing enabled the identification of all the putative pathogenicity factors
of P. ananatis LMG20103 and the use of the mutant library and post-genomic
techniques has and will allow the functional characterization of many of these
pathogenicity determinants. By this means, the mechanisms underlying the disease
caused by P. ananatis on Eucalyptus and other hosts can be better understood. With
this information, more directed and effective strategies for the control of this pathogen
and its diseases can be developed.Thesis (PhD)--University of Pretoria, 2010.
Microbiology and Plant Pathology
Unrestricted
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Moss, Stephen Paul. "The development of computational methods for large-scale comparisons and analyses of genome evolution." Thesis, University of Hull, 2015. http://hydra.hull.ac.uk/resources/hull:13083.
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The last four decades have seen the development of a number of experimental methods for the deduction of the whole genome sequences of an ever-increasing number of organisms. These sequences have in the first instance, allowed their investigators the opportunity to examine the molecular primary structure of areas of scientific interest, but with the increased sampling of organisms across the phylogenetic tree and the improved quality and coverage of genome sequences and their associated annotations, the opportunity to undertake detailed comparisons both within and between taxonomic groups has presented itself. The work described in this thesis details the application of comparative bioinformatics analyses on inter- and intra-genomic datasets, to elucidate those genomic changes, which may underlie organismal adaptations and contribute to changes in the complexity of genome content and structure over time. The results contained herein demonstrate the power and flexibility of the comparative approach, utilising whole genome data, to elucidate the answers to some of the most pressing questions in the biological sciences today. As the volume of genomic data increases, both as a result of increased sampling of the tree of life and due to an increase in the quality and throughput of the sequencing methods, it has become clear that there is a necessity for computational analyses of these data. Manual analysis of this volume of data, which can extend beyond petabytes of storage space, is now impossible. Automated computational pipelines are therefore required to retrieve, categorise and analyse these data. Chapter two discusses the development of a computational pipeline named the Genome Comparison and Analysis Toolkit (GCAT). The pipeline was developed using the Perl programming language and is tightly integrated with the Ensembl Perl API allowing for the retrieval and analyses of their rich genomic resources. In the first instance the pipeline was tested for its robustness by retrieving and describing various components of genomic architecture across a number of taxonomic groups. Additionally, the need for programmatically independent means of accessing data and in particular the need for Semantic Web based protocols and tools for the sharing of genomics resources is highlighted. This is not just for the requirements of researchers, but for improved communication and sharing between computational infrastructure. A prototype Ensembl REST web service was developed in collaboration with the European Bioinformatics Institute (EBI) to provide a means of accessing Ensembl’s genomic data without having to rely on their Perl API. A comparison of the runtime and memory usage of the Ensembl Perl API and prototype REST API were made relative to baseline raw SQL queries, which highlights the overheads inherent in building wrappers around the SQL queries. Differences in the efficiency of the approaches were highlighted, and the importance of investing in the development of Semantic Web technologies as a tool to improve access to data for the wider scientific community are discussed. Data highlighted in chapter two led to the identification of relative differences in the intron structure of a number of organisms including teleost fish. Chapter three encompasses a published, peer-reviewed study. Inter-genomic comparisons were undertaken utilising the 5 available teleost genome sequences in order to examine and describe their intron content. The number and sizes of introns were compared across these fish and a frequency distribution of intron size was produced that identified a novel expansion in the Zebrafish lineage of introns in the size range of approximately 500-2,000 bp. Further hypothesis driven analyses of the introns across the whole distribution of intron sizes identified that the majority, but not all of the introns were largely comprised of repetitive elements. It was concluded that the introns in the Zebrafish peak were likely the result of an ancient expansion of repetitive elements that had since degraded beyond the ability of computational algorithms to identify them. Additional sampling throughout the teleost fish lineage will allow for more focused phylogenetically driven analyses to be undertaken in the future. In chapter four phylogenetic comparative analyses of gene duplications were undertaken across primate and rodent taxonomic groups with the intention of identifying significantly expanded or contracted gene families. Changes in the size of gene families may indicate adaptive evolution. A larger number of expansions, relative to time since common ancestor, were identified in the branch leading to modern humans than in any other primate species. Due to the unique nature of the human data in terms of quantity and quality of annotation, additional analyses were undertaken to determine whether the expansions were methodological artefacts or real biological changes. Novel approaches were developed to test the validity of the data including comparisons to other highly annotated genomes. No similar expansion was seen in mouse when comparing with rodent data, though, as assemblies and annotations were updated, there were differences in the number of significant changes, which brings into question the reliability of the underlying assembly and annotation data. This emphasises the importance of an understanding that computational predictions, in the absence of supporting evidence, may be unlikely to represent the actual genomic structure, and instead be more an artefact of the software parameter space. In particular, significant shortcomings are highlighted due to the assumptions and parameters of the models used by the CAFE gene family analysis software. We must bear in mind that genome assemblies and annotations are hypotheses that themselves need to be questioned and subjected to robust controls to increase the confidence in any conclusions that can be drawn from them. In addition functional genomics analyses were undertaken to identify the role of significantly changed genes and gene families in primates, testing against a hypothesis that would see the majority of changes involving immune, sensory or reproductive genes. Gene Ontology (GO) annotations were retrieved for these data, which enabled highlighting the broad GO groupings and more specific functional classifications of these data. The results showed that the majority of gene expansions were in families that may have arisen due to adaptation, or were maintained due to their necessary involvement in developmental and metabolic processes. Comparisons were made to previously published studies to determine whether the Ensembl functional annotations were supported by the de-novo analyses undertaken in those studies. The majority were not, with only a small number of previously identified functional annotations being present in the most recent Ensembl releases. The impact of gene family evolution on intron evolution was explored in chapter five, by analysing gene family data and intron characteristics across the genomes of 61 vertebrate species. General descriptive statistics and visualisations were produced, along with tests for correlation between change in gene family size and the number, size and density of their associated introns. There was shown to be very little impact of change in gene family size on the underlying intron evolution. Other, non-family effects were therefore considered. These analyses showed that introns were restricted to euchromatic regions, with heterochromatic regions such as the centromeres and telomeres being largely devoid of any such features. A greater involvement of spatial mechanisms such as recombination, GC-bias across GC-rich isochores and biased gene conversion was thus proposed to play more of a role, though depending largely on population genetic and life history traits of the organisms involved. Additional population level sequencing and comparative analyses across a divergent group of species with available recombination maps and life history data would be a useful future direction in understanding the processes involved.
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Turlapaty, Sandhya. "Implementation and Performance Comparison of Some Heuristic Algorithms for Block Sorting." UNF Digital Commons, 2018. https://digitalcommons.unf.edu/etd/816.
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An implementation framework has been developed in this thesis for a well-known APX-hard combinatorial optimization problem known as Block Sorting. The motivation for the study of this problem comes from applications such as computational biology and optical character recognition. While existing Block Sorting research has been theoretically focused on the development and analysis of several approximation algorithms for Block Sorting, little or no work has been carried out thus far on the implementation of the proposed approximation algorithms. The conceptualization of an implementation framework and illustrating its use by experimenting with the existing approximation algorithms will provide means for discovering newer approaches to handling this important problem. As the main contribution, the research in this thesis provides a new greedy algorithm for Block Sorting in which each block move either reduces the number of blocks by two or three blocks, or reduces by one the number of reversals or inversions in the orig- inal permutation. Experimental results for all algorithms are also provided along with a comparison of their performance using the number of block moves and approximation ratios as performance metrics when sorting permutations of a given order, and as the order of permutations is varied. Preliminary results from the experimentation were shared at the 2017 IEEE 17th International Conference on Bioinformatics and Bioengineering (BIBE) [1]. To the best of our knowledge, this is the first work that has been focused on the implementation and experimental performance analysis of any algorithm for Block Sorting. We believe the results presented in this thesis will be useful for researchers and practitioners working in this area.
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McLeod, Donald Angus. "Comparison of the RNA genomes of persistent and parental strains of human coronavirus 229E." Thesis, University of Ottawa (Canada), 1985. http://hdl.handle.net/10393/4791.
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Marsters, Tracy Jane. "Comparison of the complete sequences of the M and F genomes of Mytilus edulis." Thesis, University of Hull, 2004. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.402495.
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Tian, Zhixi, Yanjun Yu, Feng Lin, Yeisoo Yu, Phillip SanMiguel, Rod Wing, Susan McCouch, Jianxin Ma, and Scott Jackson. "Exceptional lability of a genomic complex in rice and its close relatives revealed by interspecific and intraspecific comparison and population analysis." BioMed Central, 2011. http://hdl.handle.net/10150/610017.
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BACKGROUND:Extensive DNA rearrangement of genic colinearity, as revealed by comparison of orthologous genomic regions, has been shown to be a general concept describing evolutionary dynamics of plant genomes. However, the nature, timing, lineages and adaptation of local genomic rearrangement in closely related species (e.g., within a genus) and haplotype variation of genomic rearrangement within populations have not been well documented.RESULTS:We previously identified a hotspot for genic rearrangement and transposon accumulation in the Orp region of Asian rice (Oryza sativa, AA) by comparison with its orthologous region in sorghum. Here, we report the comparative analysis of this region with its orthologous regions in the wild progenitor species (O. nivara, AA) of Asian rice and African rice (O. glaberrima) using the BB genome Oryza species (O. punctata) as an outgroup, and investigation of transposon insertion sites and a segmental inversion event in the AA genomes at the population level. We found that Orp region was primarily and recently expanded in the Asian rice species O. sativa and O. nivara. LTR-retrotransposons shared by the three AA-genomic regions have been fixed in all the 94 varieties that represent different populations of the AA-genome species/subspecies, indicating their adaptive role in genome differentiation. However, LTR-retrotransposons unique to either O. nivara or O. sativa regions exhibited dramatic haplotype variation regarding their presence or absence between or within populations/subpopulations.CONCLUSIONS:The LTR-retrotransposon insertion hotspot in the Orp region was formed recently, independently and concurrently in different AA-genome species, and that the genic rearrangements detected in different species appear to be differentially triggered by transposable elements. This region is located near the end of the short arm of chromosome 8 and contains a high proportion of LTR-retrotransposons similar to observed in the centromeric region of this same chromosome, and thus may represent a genomic region that has recently switched from euchromatic to heterochromatic states. The haplotype variation of LTR-retrotransposon insertions within this region reveals substantial admixture among various subpopulations as established by molecular markers at the whole genome level, and can be used to develop retrotransposon junction markers for simple and rapid classification of O. sativa germplasm.
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Lantermann, Alexandra. "Comparison of Genome-Wide Nucleosome Positioning Mechanisms in Schizosaccharomyces pombe and Saccharomyces cerevisiae." Diss., lmu, 2010. http://nbn-resolving.de/urn:nbn:de:bvb:19-118784.
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Frank, Anna Carolin. "Lifestyle and Genome Evolution in Vector-Borne Bacteria : A Comparison of Three Bartonella Species." Doctoral thesis, Uppsala universitet, Molekylär evolution, 2005. http://urn.kb.se/resolve?urn=urn:nbn:se:uu:diva-5913.
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Bacterial genomes provide records of the molecular processes associated with emergence and evolution of different bacterial lifestyles. This thesis is based on whole-genome comparisons within the genus Bartonella, an excellent model system for studies of host- and vector-specificity and infection outcome in animal-associated bacteria. The louse-borne human specialist and trench fever agent Bartonella quintana was contrasted to the flea-borne generalist relatives Bartonella henselae and Bartonella grahamii, which cause asymptomatic infection in cat and mouse respectively. While B. henselae is commonly isolated from humans, and causes cat scratch disease, there is only one reported case of B. grahamii human infection. The gene complements of the three species are nested like Russian dolls with the smaller genome (B. quintana) being entirely contained in the medium sized (B. henselae), which in turned is contained in the largest (B. grahamii). Size differences reflect differences in the horizontally and vertically acquired gene content, and in the number of genus- and species- specific genes, owing to differential impact of bacteriophages and plasmids, and to different degrees of genome decay. These processes can be attributed to the three distinct lifestyles. Comparisons with other alpha-proteobacteria suggest that the Bartonella genus as a whole evolved from plant-associated species, and that horizontal transfer, in particular of genes involved in interaction with the host, played a key role in the transition to animal intracellular lifestyle. The long-term genome decay associated with this lifestyle is most advanced in the host-restricted B. quintana. The broad host-range species B. grahamii has the largest genome and the largest proportion of auxiliary DNA of the three, probably because it has access to a larger gene pool. In encodes all the known pathogenicity determinants found in the genomes of B. henselae and B. quintana, suggesting that these genes primarily evolved to facilitate colonization in the reservoir host.
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Rieber, Nora [Verfasser], and Roland [Akademischer Betreuer] Eils. "Performance comparison of four human whole-genome sequencing technologies / Nora Rieber. Betreuer: Roland Eils." Heidelberg : Universitätsbibliothek Heidelberg, 2013. http://d-nb.info/1061054527/34.
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Zhao, Zhiyu. "Robust and Efficient Algorithms for Protein 3-D Structure Alignment and Genome Sequence Comparison." ScholarWorks@UNO, 2008. http://scholarworks.uno.edu/td/851.
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Sequence analysis and structure analysis are two of the fundamental areas of bioinformatics research. This dissertation discusses, specifically, protein structure related problems including protein structure alignment and query, and genome sequence related problems including haplotype reconstruction and genome rearrangement. It first presents an algorithm for pairwise protein structure alignment that is tested with structures from the Protein Data Bank (PDB). In many cases it outperforms two other well-known algorithms, DaliLite and CE. The preliminary algorithm is a graph-theory based approach, which uses the concept of \stars" to reduce the complexity of clique-finding algorithms. The algorithm is then improved by introducing \double-center stars" in the graph and applying a self-learning strategy. The updated algorithm is tested with a much larger set of protein structures and shown to be an improvement in accuracy, especially in cases of weak similarity. A protein structure query algorithm is designed to search for similar structures in the PDB, using the improved alignment algorithm. It is compared with SSM and shows better performance with lower maximum and average Q-score for missing proteins. An interesting problem dealing with the calculation of the diameter of a 3-D sequence of points arose and its connection to the sublinear time computation is discussed. The diameter calculation of a 3-D sequence is approximated by a series of sublinear time deterministic, zero-error and bounded-error randomized algorithms and we have obtained a series of separations about the power of sublinear time computations. This dissertation also discusses two genome sequence related problems. A probabilistic model is proposed for reconstructing haplotypes from SNP matrices with incomplete and inconsistent errors. The experiments with simulated data show both high accuracy and speed, conforming to the theoretically provable e ciency and accuracy of the algorithm. Finally, a genome rearrangement problem is studied. The concept of non-breaking similarity is introduced. Approximating the exemplar non-breaking similarity to factor n1..f is proven to be NP-hard. Interestingly, for several practical cases, several polynomial time algorithms are presented.
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Pereira, Vivian Mayumi Yamassaki. "Reconstrução filogenética de procariotos com base em famílias de genes homólogos." Universidade de São Paulo, 2017. http://www.teses.usp.br/teses/disponiveis/100/100131/tde-28052017-221803/.
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A comparação de genomas é uma importante tarefa na qual a bioinformática pode ser aplicada, uma vez que ela permite a identificação de genes patogênicos, o que, por sua vez, pode auxiliar a combater ou a prevenir o surgimento de doenças. A partir da comparação de genomas, também é possível realizar a análise filogenética, que permite entender as relações evolutivas entre diferentes organismos. Em genomas de bactérias, essa análise geralmente é realizada com base no gene 16S rRNA. Entretanto, apesar de ser amplamente utilizado, filogenias com base nesse gene podem ter dificuldades para diferenciar organismos muito próximos evolutivamente. Essa importância da comparação de genomas e a necessidade de uma metodologia que permita distinguir organismos evolutivamente próximos na análise filogenética motivaram este trabalho, que teve como objetivo implementar ferramentas computacionais para identificar genes homólogos em genomas e, com base nesses genes, gerar filogenias e analisar se é possível distinguir os organismos evolutivamente próximos nessas filogenias. Para tanto, as ferramentas desenvolvidas para identificação de genes homólogos recebem resultados de alinhamentos e os filtram, de modo que dois genes são considerados homólogos se o alinhamento entre eles satisfizer os limiares definidos. Após a identificação das famílias de genes homólogos, tabelas são geradas com informações a respeito dos genes homólogos em cada genoma e, com base nessas tabelas, é possível gerar matrizes de distância e utilizar métodos de agrupamento hierárquico para a geração da filogenia ou realizar alinhamentos múltiplos com os genes identificados para posterior reconstrução filogenética. Além disso, também é possível representar os genes e famílias de genes homólogos por meio de um grafo, que pode auxiliar na escolha dos limiares para filtrar os alinhamentos. Para demonstrar e analisar a aplicabilidade das ferramentas desenvolvidas e das abordagens adotadas, experimentos foram realizados utilizando genomas de bactérias do gênero Xanthomonas, que contém um grande grupo de bactérias que causam doenças em plantas. Os resultados obtidos foram então comparados com filogenias de referência e com resultados de outros experimentos realizados. Essas comparações demonstraram que as famílias de genes homólogos podem ser úteis para distinguir genomas de organismos muito próximos evolutivamente, apesar de que essa abordagem apresentou dificuldades para separar os grupos de genomas mais distantes. Em contrapartida, na filogenia gerada a partir da região 16S rRNA, foi possível diferenciar esses organismos mais distantes, mas não foi possível distinguir os organismos muito próximos. Por fim, os experimentos realizados fornecem indícios de que as ferramentas desenvolvidas e as abordagens adotadas podem ser úteis para diferenciar genomas muito próximos evolutivamente de outros procariotos além das bactérias estudadas neste trabalhoGenome comparison is an important task on which bioinformatics can be used because it allows the identification of pathogen genes which can aid the combat of diseases and to avoid the emerging of new ones. Genome comparison also allows the phylogenetic analysis which provides the understanding of evolutional relations of different organisms. In bacterial genomes, this analysis is commonly based on 16S rRNA gene. Unfortunately, it can present some difficulties to distinguish closely related organisms. This importance of genome comparison and the necessity of a methodology to distinguish organisms that are closely related motivated this study, which aimed the development of computational tools to identify homologous genes in genomes, to use these genes to reconstruct phylogenies and to analyze if it is possible to distinguish closely related organisms on these phylogenies. To achieve this purpose, the developed tools to identify homologous genes receive the alignments results and filter it, such that two genes are homologous if their alignment satisfies the thresholds. After the identification of homologous gene families, the tools generates tables with information about the homologous genes presents in each genome and with these tables it is possible to create distance matrix to be used by hierarchical clustering methods to generate phylogenies or it is possible to perform multiple alignments with the identified genes to accomplish a phylogenetic reconstruction. Besides that, it is possible to represent the genes and homologous gene families in a graph, which can aid the choice of the thresholds to filter the alignments. To demonstrate and analyze the applicability of the developed tools and the approaches chosen in this study, experiments were performed using genomes of the bacterial genus Xanthomonas, which include a group of phytopathogenic bacteria. The results obtained were compared with reference phylogenies and with results of other experiments. These comparisons showed that homologous gene families can be used to differentiate closely related organisms, despite the fact that it presented difficulties to distinguish the groups of genomes that were evolutionarily far from each other. On the other hand, the phylogeny based on 16S rRNA region allows to distinguish the groups of genomes that were distant, but it was not possible to differentiate closely related organisms. As a conclusion, the experiments performed give pieces of evidence that the developed tools and the approaches adopted can be useful to distinguish genomes of closely related organisms of other prokaryotes besides the bacterias considered in this study
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Azuero, Andres. "Comparisons of sequential testing approaches for detection of association between disease and haplotype blocks." Thesis, Birmingham, Ala. : University of Alabama at Birmingham, 2008. https://www.mhsl.uab.edu/dt/2009r/azuero.pdf.
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