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Relevant bibliographies by topics / Genomic search / Dissertations / Theses

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Dissertations / Theses on the topic 'Genomic search'

Author: Grafiati

Published: 4 June 2021

Last updated: 1 February 2022

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1

Cameron, Michael, and mcam@mc-mc net. "Efficient Homology Search for Genomic Sequence Databases." RMIT University. Computer Science and Information Technology, 2006. http://adt.lib.rmit.edu.au/adt/public/adt-VIT20070509.162443.

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Genomic search tools can provide valuable insights into the chemical structure, evolutionary origin and biochemical function of genetic material. A homology search algorithm compares a protein or nucleotide query sequence to each entry in a large sequence database and reports alignments with highly similar sequences. The exponential growth of public data banks such as GenBank has necessitated the development of fast, heuristic approaches to homology search. The versatile and popular blast algorithm, developed by researchers at the US National Center for Biotechnology Information (N

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2

Smargon, Aaron Andrew. "An expanded search for RNA-programmable genomic engineering effectors." Thesis, Massachusetts Institute of Technology, 2016. http://hdl.handle.net/1721.1/105959.

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Thesis: S.M., Massachusetts Institute of Technology, Department of Electrical Engineering and Computer Science, 2016.<br>This electronic version was submitted by the student author. The certified thesis is available in the Institute Archives and Special Collections.<br>Cataloged from student-submitted PDF version of thesis.<br>Includes bibliographical references (pages 31-33).<br>A biocomputational pipeline was designed and implemented to mine through metagenomic datasets for novel Class 2 CRISPR (Clustered Regularly Interspaced Short Palindromic Repeat) single effectors, akin to the revoluti

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3

Sheren, Jamie Elizabeth. "Identifying functional lox sequences: A genomic search and randomized libraries." Connect to online resource, 2007. http://gateway.proquest.com/openurl?url_ver=Z39.88-2004&rft_val_fmt=info:ofi/fmt:kev:mtx:dissertation&res_dat=xri:pqdiss&rft_dat=xri:pqdiss:3273689.

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4

Lindblad, Kerstin. "Genomic studies of expanded trinucleotide repeats : focus on neuropsychiatric disorders /." Stockholm, 1998. http://diss.kib.ki.se/search/diss.se.cfm?19980904lind.

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5

Skutas, Jorie L. "Microbial and Genomic Analysis of Environmental Samples in Search of Pathogenic Salmonella." NSUWorks, 2017. http://nsuworks.nova.edu/occ_stuetd/461.

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Salmonellosis or “food poisoning” is a foodborne infection brought on by the pathogen Salmonella from the ingestion of the bacterium on contaminated foods such as vegetables. Infection from Salmonella leads to the highest incidence of hospitalizations and deaths each year, compared to any other bacterial foodborne illness. South Florida is the second largest agricultural winter vegetable producer in the United States, and contamination of vegetables is often observed in preharvest practices. A hardy bacterium, Salmonella, has been shown to live up to 6 weeks in soil and water up to 42°C withou

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Sigdel, Tara. "A Search for Zn(II) Metallochaperones in E. coli, Proteomic and Genomic Approaches." Miami University / OhioLINK, 2005. http://rave.ohiolink.edu/etdc/view?acc_num=miami1128394584.

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7

Rooney, Patrick Hugh. "A genomic approach to the study of chemoresistance." Thesis, University of Aberdeen, 2000. http://digitool.abdn.ac.uk/R?func=search-advanced-go&find_code1=WSN&request1=AAIU602009.

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This study evaluated comparative genomic hybridisation (CGH) as a tool to detect candidate regions of the genome associated with chemoresistance. Using a variation on conventional CGH, DNA from three cell lines that were resistant to thymidylate synthase (TS) inhibitors (tomudex [TDX] or 5-fluorouracil [5-FU]) and their sensitive parent cells were evaluated. In MCF-7 and H630, cells that were resistant to TDX, a specific TS inhibitor with no other known cytotoxic potential, only a single region of change (18p gain) was apparent. The third cell line H630R10, which was resistant to 5-FU, had cha

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8

Berrutti, Paula Dandara da Silva. "Genomic search of transposable elementsand their implications for the variability of pest species of fruit culture." reponame:Biblioteca Digital de Teses e Dissertações da UFRGS, 2018. http://hdl.handle.net/10183/187236.

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9

Burkhart, Tandace L. "The Search for Novel Sponge genes: Comparative Analysis of Gene Expression in Multiple Sponges." NSUWorks, 2012. http://nsuworks.nova.edu/occ_stuetd/194.

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This project focuses on the use of sponge genetic transcripts in the form of expressed sequence tags (ESTs) readily available in Genbank to search for novel genes using bioinformatics analysis tools. Marine sponge species are known to house a diversity of marine microbes and are known as the ‘living fossils’ of the animal kingdom because of the large number of ancient genes they house. Genomic mining can be a useful tool in discovering these orthologous genes. This study utilized the techniques of genomic mining of 11 previously described sponge species transcripts. The results of this study p

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10

Sun, Wenhai. "Towards Secure Outsourced Data Services in the Public Cloud." Diss., Virginia Tech, 2018. http://hdl.handle.net/10919/84396.

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Past few years have witnessed a dramatic shift for IT infrastructures from a self-sustained model to a centralized and multi-tenant elastic computing paradigm -- Cloud Computing, which significantly reshapes the landscape of existing data utilization services. In truth, public cloud service providers (CSPs), e.g. Google, Amazon, offer us unprecedented benefits, such as ubiquitous and flexible access, considerable capital expenditure savings and on-demand resource allocation. Cloud has become the virtual ``brain" as well to support and propel many important applications and system designs, for

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Ruppert, Ann-Kathrin [Verfasser], Peter [Akademischer Betreuer] Nürnberg, Peter [Akademischer Betreuer] Schneider, and Peter [Akademischer Betreuer] Kloppenburg. "Integrative functional genomic search for regulatory DNA sequence polymorphisms influencing DNA methylation and mRNA expression in hippocampal brain tissue / Ann-Kathrin Ruppert. Gutachter: Peter Nürnberg ; Peter Schneider ; Peter Kloppenburg." Köln : Universitäts- und Stadtbibliothek Köln, 2015. http://d-nb.info/1084872617/34.

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12

Zaharia, Alexandra. "Identification des motifs de voisinage conservés dans des contextes métaboliques et génomiques." Thesis, Université Paris-Saclay (ComUE), 2018. http://www.theses.fr/2018SACLS275/document.

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Cette thèse s'inscrit dans le cadre de la biologie des systèmes et porte plus particulièrement sur un problème relatif aux réseaux biologiques hétérogènes. Elle se concentre sur les relations entre le métabolisme et le contexte génomique, en utilisant une approche de fouille de graphes.Il est communément admis que des étapes enzymatiques successives impliquant des produits de gènes situés à proximité sur le chromosome traduisent un avantage évolutif du maintien de cette relation de voisinage au niveau métabolique ainsi que génomique. En conséquence, nous choisissons de nous concentrer sur la d

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13

Benedettini, Stefano <1983&gt. "Metaheuristics for Search Problems in Genomics - New Algorithms and Applications." Doctoral thesis, Alma Mater Studiorum - Università di Bologna, 2012. http://amsdottorato.unibo.it/4403/.

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In this thesis we made the first steps towards the systematic application of a methodology for automatically building formal models of complex biological systems. Such a methodology could be useful also to design artificial systems possessing desirable properties such as robustness and evolvability. The approach we follow in this thesis is to manipulate formal models by means of adaptive search methods called metaheuristics. In the first part of the thesis we develop state-of-the-art hybrid metaheuristic algorithms to tackle two important problems in genomics, namely, the Haplotype Inference

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14

Steinbeck, Rüdiger G. "Mitotic failure and genome stability in benign, premalignant and malignant human tissues /." Stockholm, 1998. http://diss.kib.ki.se/search/diss.se.cfm?19980611stei.

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15

Mecham, Jesse L. "Jumpstarting phylogenetic searches /." Diss., CLICK HERE for online access, 2006. http://contentdm.lib.byu.edu/ETD/image/etd1403.pdf.

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16

Loh, Po-Ru. "Algorithms for genomics and genetics : compression-accelerated search and admixture analysis." Thesis, Massachusetts Institute of Technology, 2013. http://hdl.handle.net/1721.1/83631.

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Thesis (Ph. D.)--Massachusetts Institute of Technology, Department of Mathematics, 2013.<br>This electronic version was submitted by the student author. The certified thesis is available in the Institute Archives and Special Collections.<br>Cataloged from student-submitted PDF version of thesis.<br>Includes bibliographical references (pages 133-139).<br>Rapid advances in next-generation sequencing technologies are revolutionizing genomics, with data sets at the scale of thousands of human genomes fast becoming the norm. These technological leaps promise to enable corresponding advances in bio

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17

Ozturk, Ozgur. "Feature extraction and similarity-based analysis for proteome and genome databases." The Ohio State University, 2007. http://rave.ohiolink.edu/etdc/view?acc_num=osu1190138805.

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18

Kovaliovas, Viktoras. "Genomų palyginimo algoritmų tyrimas." Master's thesis, Lithuanian Academic Libraries Network (LABT), 2005. http://vddb.library.lt/obj/LT-eLABa-0001:E.02~2005~D_20050523_134443-96340.

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To understand evolution, and to discover how different species are related, gene order analysis is a useful tool. Problems in this area can usually be formulated in a combinatorial language. We regard genomes as signed, or unsigned permutations, and thus evolutionary operations like inversions (reversing the order of a segment of genes) are easy to describe combinatorially. A commonly studied problem is to determine the evolutionary distance between two species. This is estimated by several combinatorial distances between gene order permutations, for instance the inversion distance. The main o

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19

Wold, Håkon Hjelde. "Can Genome Information be used to Guide Evolutionary Search?" Thesis, Norges teknisk-naturvitenskapelige universitet, Institutt for datateknikk og informasjonsvitenskap, 2013. http://urn.kb.se/resolve?urn=urn:nbn:no:ntnu:diva-23599.

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Uniform cellular automata have been evolved as phenotypes from zygotes using an extensive rule table as the genotype. This is used to simulate complex systems which could impact future hardware development and programming. This work falls within the field of Evolutionary and Developmental Systems (EvoDevo). Genome parameters are used in a genetic algorithm to try to reduce the number of generations needed to find a genome with a given complexity. Lambda parameter has been used inside the fitness function and produced promising results. Lambda has also been used to discard genomes before they a

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20

Holley, Guillaume [Verfasser], and Jens [Akademischer Betreuer] Stoye. "Pan-genome Search and Storage / Guillaume Holley ; Betreuer: Jens Stoye." Bielefeld : Universitätsbibliothek Bielefeld, 2018. http://d-nb.info/1155302710/34.

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21

Bailey, David M. D. "Genome mapping in a search for a sex determining gene." Thesis, University of Cambridge, 1995. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.361752.

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22

Bhattaru, Srinivasa Aditya. "Design, testing, and validation of the search for Extra-Terrestrial Genomes instrument." Thesis, Massachusetts Institute of Technology, 2018. http://hdl.handle.net/1721.1/119060.

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Thesis: S.M., Massachusetts Institute of Technology, Department of Aeronautics and Astronautics, 2018.<br>Cataloged from PDF version of thesis.<br>Includes bibliographical references (pages 75-78).<br>The development of any spaceflight instrument involves a systematic, iterative process of design, testing, and validation. This ensures that the system developed will meet the needs of stakeholders while minimizing costs and risks. Here, the needs for a life-detection instrument targeting nucleic acids are identified, the objectives for that instrument are determined, and system engineering analy

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23

Keller, Brigitte D. "Search for new steroid hormone metabolizing enzymes functional genomics of the short chain dehydrogenase, reductase superfamily /." [S.l.] : [s.n.], 2006. http://mediatum2.ub.tum.de/doc/603773/document.pdf.

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24

Gardeux, Vincent. "Conception d'heuristiques d'optimisation pour les problèmes de grande dimension : application à l'analyse de données de puces à ADN." Phd thesis, Université Paris-Est, 2011. http://tel.archives-ouvertes.fr/tel-00676449.

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Cette thèse expose la problématique récente concernant la résolution de problèmes de grande dimension. Nous présentons les méthodes permettant de les résoudre ainsi que leurs applications, notamment pour la sélection de variables dans le domaine de la fouille de données. Dans la première partie de cette thèse, nous exposons les enjeux de la résolution de problèmes de grande dimension. Nous nous intéressons principalement aux méthodes de recherche linéaire, que nous jugeons particulièrement adaptées pour la résolution de tels problèmes. Nous présentons ensuite les méthodes que nous avons dévelo

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25

Thompson, Katherine L. "Using ancestral information to search for quantitative trait loci in genome-wide association studies." The Ohio State University, 2013. http://rave.ohiolink.edu/etdc/view?acc_num=osu1372410951.

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26

Kusuma, Pradiptajati. "In search of Asian Malagasy ancestors in Indonesia." Thesis, Toulouse 3, 2017. http://www.theses.fr/2017TOU30109/document.

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L'Indonésie a été l'objet de la dispersion Austronésienne qui a débuté il y a environ 5000 ans depuis Taiwan, se propager à travers les Philippines et l'Indonésie, puis toucher l'Océanie à l'est, et à Madagascar à l'ouest. Malgré de nombreuses recherches en génétique sur la dispersion Austronésienne vers l'est, il y a très peu de données sur la dispersion vers l'ouest, laissant sans réponse de nombreuses questions, liées notamment au peuplement de Madagascar. Reposant sur l'analyse des données culturelles et biologiques, les populations d'Indonésie semblent avoir joué un rôle majeur dans la co

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27

Johnson, Andrew Danner. "Search for functional alleles in the human genome with focus on cardiovascular disease candidate genes." Columbus, Ohio : Ohio State University, 2007. http://rave.ohiolink.edu/etdc/view?acc%5Fnum=osu1187018497.

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28

Feng, Xiaopeng. "Chicken growth hormone receptor and growth hormone : search for genetic variants which affect commercially important traits." Thesis, McGill University, 1996. http://digitool.Library.McGill.CA:80/R/?func=dbin-jump-full&object_id=42028.

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Chicken genomic DNA containing 5 kb of the 5$ sp prime$ end of the growth hormone (GH) receptor gene and 12 kb of the region up-stream was cloned and a restriction map was constructed. Using subcloned fragments as probes, a HindIII polymorphism was detected in both egg layer and in meat-type chickens. This polymorphic site was mapped at 7 kb up-stream of the coding region of the GH-receptor gene and a PCR assay for the polymorphism was developed to facilitate genotyping of large numbers of chickens.<br>Alleles of the GH-receptor gene and the GH gene were analyzed for association with traits in

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Forgetta, Vincenzo. "Systematic search for Salmonella-susceptibility quantitative trait loci in the chicken using a whole genome scan approach." Thesis, McGill University, 2001. http://digitool.Library.McGill.CA:80/R/?func=dbin-jump-full&object_id=33758.

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The goal of this project is to identify QTL involved in Salmonella -susceptibility in the chicken. Salmonellosis is one of the most common causes of food poisoning in humans and is frequently caused by the ingestion of Salmonella-contaminated poultry products. Identification of QTL responsible for Salmonella-susceptibility may lead to more efficient control strategies, and selection against genes that may lead to increased risk of transmission. The genome scan was performed on a selection of 425 backcross progeny, (W1 x C) F1 x C, derived from C Salmonella-susceptible and W1 Salmonella-resista

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Zhang, Youming. "A genome-wide search for asthma-associated quantitative traits loci in a mouse model of allergic asthma." Thesis, University of Oxford, 1999. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.312554.

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31

Cénac, Peggy. "Étude statistique de séquences biologiques et convergence de martingales." Toulouse 3, 2006. http://www.theses.fr/2006TOU30065.

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Le système dynamique Chaos Game Representation associe à une suite de lettres dans un alphabet fini, une mesure empirique sur un ensemble. Fournit-elle plus d'information que les méthodes de comptage de mots classiques ? A partir d'une caractérisation basée sur la CGR, on propose une nouvelle famille de tests donnant l'ordre d'une chaîne de Markov homogène. On définit ensuite une construction d'arbres digitaux de recherche, inspirés par la CGR, en insérant successivement les préfixes retournés d'une chaîne de Markov. On montre que les longueurs des branches critiques se comportent, au premier

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32

Ross-Adams, Helen. "A genome-wide association study into ischaemic stroke using DNA pools and microarrays." Thesis, University of Aberdeen, 2006. http://digitool.abdn.ac.uk/R?func=search-advanced-go&find_code1=WSN&request1=AAIU222719.

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The main aim of this project was to identify likely candidate genes in ischaemic stroke from a population in North-East Scotland. SNP allele frequencies were investigated for significant differences between case and control pools to identify chromosomal regions likely to contain relevant genes. In this way, 43 candidate genes for ischaemic stroke were identified. Two had previously been found by other studies (ALOX5AP and PDE4D), and several interact with each other in a particular biochemical pathway. Moreover, the majority of genes identified could be grouped into four main disease processe

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Gaspar, Manuel Augusto Ribeiro. "Automatic system for approximate and noncontiguous DNA sequences search." Master's thesis, Universidade de Aveiro, 2017. http://hdl.handle.net/10773/23810.

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Mestrado em Engenharia Eletrónica e Telecomunicações<br>A capacidade de efectuar pesquisas de sequências de ADN similares a outras contidas numa sequência maior, tal como um cromossoma, tem um papel muito importante no estudo de organismos e na possível ligação entre espécies diferentes. Apesar da existência de várias técnicas e algoritmos, criados com o intuito de realizar pesquisas de sequência, este problema ainda está aberto ao desenvolvimento de novas ferramentas que possibilitem melhorias em relação a ferramentas já existentes. Esta tese apresenta uma solução para pesquisa de seq

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34

Milanius, Michelle, and Sofie Kullman. "Utnyttjar konsumenter möjligheten att agera rationellt? : En uppsats om konsumenters sökbeteende inför ett köp med avseende på irrationella köpbeslut eller möjliggörandet av rationella köpbeslut genom informationssökningsprocessen." Thesis, Örebro universitet, Handelshögskolan vid Örebro Universitet, 2014. http://urn.kb.se/resolve?urn=urn:nbn:se:oru:diva-34752.

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The buying decision process describes how the consumer makes a purchase decision through a rational process (Markin, 1979) and an understanding for how consumers make a purchase decision can according to Sands et al. (2010) be obtained by increased knowledge for the information search process (the second part of the buying decision process) before a purchase. Today’s society offers great opportunity to obtain information (Rahim & Clemens, 2012; Bawden & Robinson, 2009) and by that there are in other words good opportunities for a rational acting by the consumers. However, there are fac

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Morra, Erica, and Lisa Zenker. "Chapter 1: In Search of Innate Leadership : Discovering, Evaluating and Understanding Innateness." Thesis, Linnéuniversitetet, Institutionen för organisation och entreprenörskap (OE), 2014. http://urn.kb.se/resolve?urn=urn:nbn:se:lnu:diva-34622.

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Every individual is born with different natural competencies that can be honed by both voluntary and involuntary environmental stimuli. The response our genotype decides to make, if any, towards those stimuli, determines how well our competencies develop. Each person’s coding and variations of genes will result in unique qualities in their phenotype, or physical structure. As a result, a person has various traits that are displayed through their behavior. DNA is genetically shown to express itself through traits by up to 75%. This leaves a sort of buffer of around 25%. This region is available

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Paulino, Rosangela Clara. "Detecção molecular de Giardia sp em amostras fecais e água : extração de DNA genomico, PCR e RFLP /." oai:ufpr.br:234179, 2005. http://200.17.209.5:8000/cgi-bin/gw_42_13/chameleon.42.13a?host=localhost%201111%20DEFAULT&sessionid=VTLS&function=CARDSCR&search=KEYWORD&pos=1&u1=12101&t1=234179.

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Orientadora : Vanete Thomaz Soccol<br>Tese (doutorado) - Universidade Federal do Paraná, Setor de Tecnologia, Programa de Pós-Graduaçao em Processos Biotecnológicos. Defesa: Curitiba, 2005<br>Inclui bibliografia<br>Área de concentração: Saude humana e animal

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Sung, Po Yi, and 宋柏誼. "Genomic DNA Sequence Visualization and Similarity Search." Thesis, 2005. http://ndltd.ncl.edu.tw/handle/91517210134622504786.

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碩士<br>國立中正大學<br>通訊工程研究所<br>91<br>Genomic DNA sequences can been represented as long text data composed of alphabets A, C, T and G. These sequences present visualization challenges due to their length and complexity. In this paper, we proposed a visual technique called VBP (Visualization by Pentahedrons) algorithm to visualize and analyze similarity of DNA sequences. Here, a Markov chain model is employed to calculate the state transition probabilities of DNA sequences and map them into four different pentahedrons. According to these four pentahedrons, a three-dimensional trajectory can be draw

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Lin, Heshan. "High performance parallel and distributed genomic sequence search." 2009. http://www.lib.ncsu.edu/theses/available/etd-03132009-172048/unrestricted/etd.pdf.

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Bhavsar, Rajul D. "Search-Optimized Disk Layouts For Suffix-Tree Genomic Indexes." Thesis, 2011. http://etd.iisc.ernet.in/handle/2005/2124.

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Over the last decade, biological sequence repositories have been growing at an exponential rate. Sophisticated indexing techniques are required to facilitate efficient searching through these humongous genetic repositories. A particularly attractive index structure for such sequence processing is the classical suffix-tree, a vertically compressed trie structure built over the set of all suffixes of a sequence. Its attractiveness stems from its linearity properties -- suffix-tree construction times are linear in the size of the indexed sequences, while search times are linear in the size of the

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Riascos, John Jaime. "A genomic-based search for novel soybean (Glycine max L.) allergens." 2009. http://www.lib.ncsu.edu/theses/available/etd-12172008-120356/unrestricted/etd.pdf.

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Mosig, Axel, Katrin Sameith, and Peter F. Stadler. "Fragrep: An Efficient Search Tool for Fragmented Patterns in Genomic Sequences." 2006. https://ul.qucosa.de/id/qucosa%3A32010.

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Many classes of non-coding RNAs (ncRNAs; including Y RNAs, vault RNAs, RNase P RNAs, and MRP RNAs, as well as a novel class recently discovered in Dictyostelium discoideum) can be characterized by a pattern of short but well-conserved sequence elements that are separated by poorly conserved regions of sometimes highly variable lengths. Local alignment algorithms such as BLAST are therefore ill-suited for the discovery of new homologs of such ncRNAs in genomic sequences. The Fragrep tool instead implements an efficient algorithm for detecting the pattern fragments that occur in a given order. F

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Bataille, Alain R. "Genome wide search for glycine metabolism genes." Thesis, 2003. http://spectrum.library.concordia.ca/2260/1/MQ83846.pdf.

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The yeast Saccharomyces cerevisiae uses glycine for the synthesis of activated one-carbon units and nitrogen metabolism. The homozygous diploid set of deletion strains includes strains deleted from all the S. cerevisiae non-essential genes (about 4700). This deletion set was screened for strains exhibiting a growth phenotype when glycine was used as the sole nitrogen source (Gmin medium). This screen identified a total of 321 strains. Within the 321 strains, 250 showed a growth defect on Gmin (G- phenotype) whereas 71 exhibited better growth on Gmin (G+ phenotype). Further high-density colony-

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Abhinav, K. V. "Further Structural Studies on Jacalin and Genomics Search for Mycobacterial and Archeal Lectins." Thesis, 2016. http://etd.iisc.ernet.in/handle/2005/2858.

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This thesis consists of two parts. The first part is concerned with further structural and related studies of jacalin, one of the two lectins found in jack fruit seeds. The second part deals with the search of mycobacterial and archeal genomes for lectins. The β-prism I fold was identified as a lectin fold through the X-ray analysis of jacalin way back in 1996. Subsequent structural studies on jacalin are described in the first chapter in context of the overall efforts on lectins with particular reference to those on lectins with β-prism I fold. The structure of jacalin has been thoroughly ch

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Stinson, E. O. "Implementation of vectorbase components ensEMBL genome browser, search , and database tools /." 2007. http://etd.nd.edu/ETD-db/theses/available/etd-09262007-153616/.

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Garvilles, Ronald-Garingalao, and 蓋羅納. "Genome-wide methylation pattern search in Prader-Willi Syndrome (PWS) patients." Thesis, 2011. http://ndltd.ncl.edu.tw/handle/59827189279715437068.

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碩士<br>中原大學<br>生物科技研究所<br>99<br>Prader-Willi Syndrome (PWS) is a neurodevelopmental disorder caused by lack of functional paternal copy of 15q11-q13. Epigenetic aberrations due to genomic imprinting defect leads to the absence expression of paternally-inherited genes. This study aims to provide an overview of the methylation status of the whole-genome among PWS patients. A novel method PCR Selective Suppression Hybridization (PSSH) was employed to screen the putative genes that are differentially methylated among PWS patients but not in normal individuals. This method utilizes hybridization of

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Chen, Ko-Fan, and 陳克帆. "Whole Genome Search of Candidate Hypoxia Response Genes by Bioinformatic Methodology." Thesis, 2005. http://ndltd.ncl.edu.tw/handle/70822334854372391625.

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碩士<br>國立成功大學<br>生理學研究所<br>93<br>Hypoxia is the reduction of environmental oxygen In absent of oxygen, hypoxia inducible factor-1 a (HIF-1a) dimerizes with HIF-1b and binds to the hypoxia response element (HRE) on the target DNA sequence. HIF-1a regulated genes have been found to be involved in cell proliferation, angiogenesis, glycolysis, apoptosis, and tumor formation. The HRE with a short core sequence “RCGTG” is necessary but not sufficient to be bound by HIF-1a. The flanking region also determines the binding activity. Accordingly, the 20 well known HREs were retrieved, aligned, and built

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Wittig, Michael David. "Search for selection pressures associated with aggregation propensity following whole genome duplication in S.cerevisiae." Thesis, 2011. http://hdl.handle.net/2152/ETD-UT-2011-12-4528.

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It has been theorized that most proteins are under selection pressure to be soluble in crowded cellular spaces. To maintain solubility a proteins’ aggregation propensity should be inversely proportional to their maximum likely concentration. This theory was examined by comparing the proteome of the model organism S. cerevisiae, which has previously undergone a Whole Genome Duplication (WGD) event to the proteome of the closely related yeast K. waltii, which has not undergone WGD. This comparison revealed the following: 1) Predicted aggregation propensities are higher in S. cerevisiae than K.

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Keller, Brigitte D. [Verfasser]. "Search for new steroid hormone metabolizing enzymes : functional genomics of the short chain dehydrogenase, reductase superfamily / Brigitte D. Keller." 2006. http://d-nb.info/985501227/34.

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Harrington, Dean J., and I. C. Sutcliffe. "Pattern searches for the identification of putative lipoprotein genes in Gram positive bacterial genomes." 2002. http://hdl.handle.net/10454/3167.

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No<br>N-terminal lipidation is a major mechanism by which bacteria can tether proteins to membranes and one which is of particular importance to Gram-positive bacteria due to the absence of a retentive outer membrane. Lipidation is directed by the presence of a cysteine-containing `lipobox' within the lipoprotein signal peptide sequence and this feature has greatly facilitated the identification of putative lipoproteins by gene sequence analysis. The properties of lipoprotein signal peptides have been described previously by the Prosite pattern PS00013. Here, a dataset of 33 experimentally ver

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Hertel, Jana, Jong Danielle de, Manja Marz, Dominic Rose, Hakim Tafer, Andrea Tanzer, Bernd Schierwater, and Peter F. Stadler. "Non-coding RNA annotation of the genome of Trichoplax adhaerens." 2009. https://ul.qucosa.de/id/qucosa%3A32946.

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A detailed annotation of non-protein coding RNAs is typically missing in initial releases of newly sequenced genomes. Here we report on a comprehensive ncRNA annotation of the genome of Trichoplax adhaerens, the presumably most basal metazoan whose genome has been published to-date. Since blast identified only a small fraction of the best-conserved ncRNAs—in particular rRNAs, tRNAs and some snRNAs—we developed a semi-global dynamic programming tool, GotohScan, to increase the sensitivity of the homology search. It successfully identified the full complement of major and minor spliceosomal snRN

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