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Dissertations / Theses on the topic 'Sequence profiles'
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1
Chan, Yin-leung. "Identification of bacteria with ambiguous biochemical profiles by 16S ribosomal RNA gene sequencing." Hong Kong : University of Hong Kong, 2001. http://sunzi.lib.hku.hk:8888/cgi-bin/hkuto%5Ftoc%5Fpdf?B23373209.
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陳賢良 and Yin-leung Chan. "Identification of bacteria with ambiguous biochemical profiles by 16S ribosomal RNA gene sequencing." Thesis, The University of Hong Kong (Pokfulam, Hong Kong), 2001. http://hub.hku.hk/bib/B3197028X.
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Menlove, Kit J. "Model Detection Based upon Amino Acid Properties." BYU ScholarsArchive, 2010. https://scholarsarchive.byu.edu/etd/2253.
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Similarity searches are an essential component to most bioinformatic applications. They form the bases of structural motif identification, gene identification, and insights into functional associations. With the rapid increase in the available genetic data through a wide variety of databases, similarity searches are an essential tool for accessing these data in an informative and productive way. In our chapter, we provide an overview of similarity searching approaches, related databases, and parameter options to achieve the best results for a variety of applications. We then provide a worked example and some notes for consideration. Homology detection is one of the most basic and fundamental problems at the heart of bioinformatics. It is central to problems currently under intense investigation in protein structure prediction, phylogenetic analyses, and computational drug development. Currently discriminative methods for homology detection, which are not readily interpretable, are substantially more powerful than their more interpretable counterparts, particularly when sequence identity is very low. Here I present a computational graph-based framework for homology inference using physiochemical amino acid properties which aims to both reduce the gap in accuracy between discriminative and generative methods and provide a framework for easily identifying the physiochemical basis for the structural similarity between proteins. The accuracy of my method slightly improves on the accuracy of PSI-BLAST, the most popular generative approach, and underscores the potential of this methodology given a more robust statistical foundation.
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Savel, Daniel M. "Towards a Human Genomic Coevolution Network." Case Western Reserve University School of Graduate Studies / OhioLINK, 2018. http://rave.ohiolink.edu/etdc/view?acc_num=case1524241451267546.
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Chen, Sharon S. "Peptide sequence assignments by probabilistic peptide profile matching to an annotated peptide database /." Thesis, Connect to this title online; UW restricted, 2005. http://hdl.handle.net/1773/8084.
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Reysset, Aurelien. "Conception préliminaire d'actionneurs électromécaniques - outils d'aide à la spécification et à la génération de procédures de dimensionnement pour l'optimisation." Thesis, Toulouse, INSA, 2015. http://www.theses.fr/2015ISAT0003/document.
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Cette thèse a pour objectif d’apporter un ensemble d’outils logiciels s’inscrivant dans une méthodologie globale de conception de systèmes mécatroniques. Elle arrive en complément de travaux déjà menés au sein du laboratoire sur le pré-dimensionnement d’actionneurs aéronautiques de nouvelle génération : les actionneurs électromécaniques (EMA). Cette technologie apporte de nouvelles problématiques qui forcent les ingénieurs à modifier leur processus de développement et ce dès la phase de spécification où des profils de mission devront être générés/transformés/analysés de manière à simplifier la conception et assurer leur validation. Une toolbox Simulink a donc été créée dans cette thèse pour répondre à ce besoin de transformation de l’information entre avionneur et systémier. Comme tout système embarqué, le concepteur fait face à des compromis entre performances, durée de vie et intégration, qui peuvent se résumer à un problème d’optimisation décrit par un ensemble d’équations et de contraintes. Un effort particulier de description a été mené sur le conditionnement de ces équations sous la forme d’un séquencement de calculs explicites adaptés aux algorithmes d’optimisation. La méthode et son implémentation logicielle, toutes deux basées sur la théorie des graphes, interagissent avec le concepteur de manière à l’informer des erreurs de singularité ou de bouclages algébriques apparaissant dans son problème et à lui fournir des pistes de résolution. Pour finir, des études de pré-dimensionnement d’actionneurs de train d’atterrissage et de surfaces de vol primaires (aileron et spoiler), réalisées dans le cadre de cette thèse, dresseront les possibilités offertes par cette approche innovante : conception intégrée avec une cinématique complexe, conception collaborative pluri-partenaires découplée, utilisation de surfaces de réponse pour accélérer l’optimisationThe aim of this thesis is to bring a package of software tools included in a whole methodology dealing with mechatronic systems design. It comes as an add-on to the work already carried out at the laboratory in the field of the new generation of aircraft actuation systems: electromechanical actuators (EMA). This technology triggers new problematics leading the engineers to modify their development process as early as the specification phase, when mission profiles have to be generated/transformed/analyzed in order to simplify the design and ensure the validation step. Thus a Simulink toolbox has been created to meet the need for an information translator working as an intermediate between airframer and system-supplier. As for all the embedded systems, the designer has to face some performance-lifetime-integration trade-off, which can be considered as an optimization problem described by a set of equations and constraints. Particular attention is paid here to the conditioning of those explicit equations in order to obtain a standardized calculation sequence adapted to many optimization algorithms. The method and implemented software, both based on the graph theory, interact with the designer to inform him on the possible singularity and algebraic loop issues, providing some leads for their resolution. Finally, some preliminary sizing studies of landing gear and primary flight control surfaces (aileron and spoiler) actuation systems are presented to highlight the possibilities brought out by this innovative approach: integrated design with complex kinematics, collaborative multi-partners design, use of response surfaces to speed up the optimization
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Zhang, Yue. "Detection copy number variants profile by multiple constrained optimization." HKBU Institutional Repository, 2017. https://repository.hkbu.edu.hk/etd_oa/439.
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Copy number variation, causing by the genome rearrangement, generally refers to the copy numbers increased or decreased of large genome segments whose lengths are more than 1kb. Such copy number variations mainly appeared as the sub-microscopic level of deletion and duplication. Copy number variation is an important component of genome structural variation, and is one of pathogenic factors of human diseases. Next generation sequencing technology is a popular CNV detection method and it has been widely used in various fields of life science research. It possesses the advantages of high throughput and low cost. By tailoring NGS technology, it is plausible to sequence individual cells. Such single cell sequencing can reveal the gene expression status and genomic variation profile of a single-cell. Single cell sequencing is promising in the study of tumor, developmental biology, neuroscience and other fields. However, there are two challenging problems encountered in CNV detection for NGS data. The first one is that since single-cell sequencing requires a special genome amplification step to accumulate enough samples, a large number of bias is introduced, making the calling of copy number variants rather challenging. The performances of many popular copy number calling methods, designed for bulk sequencings, are not consistent and cannot be applied on single-cell sequenced data directly. The second one is to simultaneously analyze genome data for multiple samples, thus achieving assembling and subgrouping similar cells accurately and efficiently. The high level of noises in single-cell-sequencing data negatively affects the reliability of sequence reads and leads to inaccurate patterns of variations. To handle the problem of reliably finding CNVs in NGS data, in this thesis, we firstly establish a workflow for analyzing NGS and single-cell sequencing data. The CNVs identification is formulated as a quadratic optimization problem with both constraints of sparsity and smoothness. Tailored from alternating direction minimization (ADM) framework, an efficient numerical solution is designed accordingly. The proposed model was tested extensively to demonstrate its superior performances. It is shown that the proposed approach can successfully reconstruct CNVs especially somatic copy number alteration patterns from raw data. By comparing with existing counterparts, it achieved superior or comparable performances in detection of the CNVs. To tackle this issue of recovering the hidden blocks within multiple single-cell DNA-sequencing samples, we present an permutation based model to rearrange the samples such that similar ones are positioned adjacently. The permutation is guided by the total variational (TV) norm of the recovered copy number profiles, and is continued until the TV-norm is minimized when similar samples are stacked together to reveal block patterns. Accordingly, an efficient numerical scheme for finding this permutation is designed, tailored from the alternating direction method of multipliers. Application of this method to both simulated and real data demonstrates its ability to recover the hidden structures of single-cell DNA sequences.
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Houston, Alice Elizabeth Dashwood. "On binary sequences with specific linear complexity and correlation properties." Thesis, Royal Holloway, University of London, 1995. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.307031.
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For many applications, such as cryptography and digital communications, binary sequences with certain specific properties are required. These include a balance of 0's and 1's in a period, ideal runs frequencies, good auto- and cross-correlation spectra, and high linear complexity. Perfect Linear Complexity Profile sequences (PLCPs) have the linear complexity of all subsequences (starting with the first bit) equal to half the length of the subsequence (this is the expected value for a random sequence). We investigate the density - proportion of ones - of finite length PLCPs, both in general and for specific examples. We gain results on the average, maximal and minimal densities, as well as their limits as the length tends to infinity. We also study whether the PLCP property is preserved under various decimations. PLCPs are characterised by a simple linear recurrence modulo 2. We look at similar "nearly" perfect profiles and characterise sequences with these profiles in terms of similar recurrences. Also sequences with a PLCP up to a point and then constant complexity are characterised in terms of the convergents in the continued fraction expansion of the generating function of PLCPs, and we look briefly at their corresponding periods. Sequences with bounded jumps in their linear complexity are discussed and a method of generating them is suggested. The interleaving of shifts of a sequence with out-of-phase auto-correlation equal to -1 and balance, in a specific order, seems to be a fundamental method of generating longer sequences with this auto-correlation property. It is shown that two pairs of families of these sequences, derived in different ways, are in fact equivalent. The analysis highlights the general method mentioned above, and so provides examples of families of sequences with 2-valued auto-correlation by changing the ingredients in the interleaving pattern. We also look at the cross-correlation of sequences with this interleaved structure.
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Ohlson, Tomas. "The use of evolutionary information in protein alignments and homology identification." Doctoral thesis, Stockholm : Stockholm Bioinformatics Center, Stockholm University, 2006. http://urn.kb.se/resolve?urn=urn:nbn:se:su:diva-812.
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Guney, Tacettin Dogacan. "Prediction Of Protein-protein Interactions From Sequence Using Evolutionary Relations Of Proteins And Species." Master's thesis, METU, 2009. http://etd.lib.metu.edu.tr/upload/12611058/index.pdf.
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Prediction of protein-protein interactions is an important part in understanding the biological processes in a living cell. There are completely sequenced organisms that do not yet have experimentally verified protein-protein interaction networks. For such organisms, we can not generally use a supervised method, where a portion of the protein-protein interaction network is used as training set. Furthermore, for newly-sequenced organisms, many other data sources, such as gene expression data and gene ontology annotations, that are used to identify protein-protein interaction networks may not be available. In this thesis work, our aim is to identify and cluster likely protein-protein interaction pairs using only sequence of proteins and evolutionary information. We use a protein&rsquos phylogenetic profile because the co-evolutionary pressure hypothesis suggests that proteins with similar phylogenetic profiles are likely to interact. We also divide phylogenetic profile into smaller profiles based on the evolutionary lines. These divided profiles are then used to score the similarity between all possible protein pairs. Since not all profile groups have the same number of elements, it is a difficult task to assess the similarity between such pairs. We show that many commonly used measures do not work well and that the end result greatly depends on the type of the similarity measure used. We also introduce a novel similarity measure. The resulting dense putative interaction network contains many false-positive interactions, therefore we apply the Markov Clustering algorithm to cluster the protein-protein interaction network and filter out the weaker edges. The end result is a set of clusters where proteins within the clusters are likely to be functionally linked and to interact. While this method does not perform as well as supervised methods, it has the advantage of not requiring a training set and being able to work only using sequence data and evolutionary information. So it can be used as a first step in identifying protein-protein interactions in newly-sequenced organisms.
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Rouzic, Sylvain. "Les logiques de professionnalisation des entraîneurs sportifs : entre modèles socioculturels et profils individuels." Thesis, Paris, CNAM, 2015. http://www.theses.fr/2015CNAM1014/document.
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Le statut et la fonction de l'entraîneur sportif se sont progressivement développés avec la naissance du sport moderne, à partir de la fin du XVIIIe siècle. Du début du XXe siècle à aujourd'hui, le modèle le plus prégnant est celui du technicien de « terrain » dont les méthodes se construisent avant tout sous l'influence socioculturelle dans laquelle il est « baigné ». À partir des années 1980, le processus de professionnalisation qui s'est développé a eu comme conséquence une subdivision des modèles stabilisés en nombreux profils individuels, qui vont bien au-delà du simple triptyque technicien-meneur d'hommes-stratège, mis en avant dans les différentes représentations de sens commun. L'analyse des discours de vingt entraîneurs sportifs, choisis pour représenter au mieux l'ensemble de cette population, nous permet de confirmer les modèles socioculturels connus, et de faire apparaître des profils individuels variés. Elle permet surtout de mettre en évidence l'ensemble des logiques de professionnalisation de cette population. Qu'elles soient communicationnelles, techniques, organisationnelles ou de formation, ces logiques ont comme intérêt scientifique de montrer comment les entraîneurs sportifs se construisent professionnellement aujourd'huiThe status and function of the sport coach have steadily developed since the birth of modern-era sport, in the late 18th century. From the early 20th c. to the present day, the most significant model is that of the field technician whose methods have been built under the influence of his or her social and cultural background. The 1980s saw the emergence of a professionalisation process which subdivided the existing patterns into a variety of individual models, going further beyond the mere three-dimensional combination of the technician-leader-strategist that seems to be the most received representation. Material collected from twenty interviews with sport trainers who were chosen as the best possible sample of the population has been analyzed. This analysis both confirms the received social and cultural patterns and highlights various individual models. In particular, it traces all the logical sequences that define the professionalisation of the population.Be they related to communication, techniques, organisation or training, these sequences find their scientific value in the demonstration they make of how sport coaching takes shape nowadays
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Zhao, Mengyao. "Genomic variation detection using dynamic programming methods." Thesis, Boston College, 2014. http://hdl.handle.net/2345/bc-ir:104357.
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Thesis advisor: Gabor T. MarthBackground: Due to the rapid development and application of next generation sequencing (NGS) techniques, large amounts of NGS data have become available for genome-related biological research, such as population genetics, evolutionary research, and genome wide association studies. A crucial step of these genome-related studies is the detection of genomic variation between different species and individuals. Current approaches for the detection of genomic variation can be classified into alignment-based variation detection and assembly-based variation detection. Due to the limitation of current NGS read length, alignment-based variation detection remains the mainstream approach. The Smith-Waterman algorithm, which produces the optimal pairwise alignment between two sequences, is frequently used as a key component of fast heuristic read mapping and variation detection tools for next-generation sequencing data. Though various fast Smith-Waterman implementations are developed, they are either designed as monolithic protein database searching tools, which do not return detailed alignment, or they are embedded into other tools. These issues make reusing these efficient Smith-Waterman implementations impractical. After the alignment step in the traditional variation detection pipeline, the afterward variation detection using pileup data and the Bayesian model is also facing great challenges especially from low-complexity genomic regions. Sequencing errors and misalignment problems still influence variation detection (especially INDEL detection) a lot. The accuracy of genomic variation detection still needs to be improved, especially when we work on low- complexity genomic regions and low-quality sequencing data. Results: To facilitate easy integration of the fast Single-Instruction-Multiple-Data Smith-Waterman algorithm into third-party software, we wrote a C/C++ library, which extends Farrar's Striped Smith-Waterman (SSW) to return alignment information in addition to the optimal Smith-Waterman score. In this library we developed a new method to generate the full optimal alignment results and a suboptimal score in linear space at little cost of efficiency. This improvement makes the fast Single-Instruction-Multiple-Data Smith-Waterman become really useful in genomic applications. SSW is available both as a C/C++ software library, as well as a stand-alone alignment tool at: https://github.com/mengyao/Complete- Striped-Smith-Waterman-Library. The SSW library has been used in the primary read mapping tool MOSAIK, the split-read mapping program SCISSORS, the MEI detector TAN- GRAM, and the read-overlap graph generation program RZMBLR. The speeds of the mentioned software are improved significantly by replacing their ordinary Smith-Waterman or banded Smith-Waterman module with the SSW Library. To improve the accuracy of genomic variation detection, especially in low-complexity genomic regions and on low-quality sequencing data, we developed PHV, a genomic variation detection tool based on the profile hidden Markov model. PHV also demonstrates a novel PHMM application in the genomic research field. The banded PHMM algorithms used in PHV make it a very fast whole-genome variation detection tool based on the HMM method. The comparison of PHV to GATK, Samtools and Freebayes for detecting variation from both simulated data and real data shows PHV has good potential for dealing with sequencing errors and misalignments. PHV also successfully detects a 49 bp long deletion that is totally misaligned by the mapping tool, and neglected by GATK and Samtools. Conclusion: The efforts made in this thesis are very meaningful for methodology development in studies of genomic variation detection. The two novel algorithms stated here will also inspire future work in NGS data analysis
Thesis (PhD) — Boston College, 2014
Submitted to: Boston College. Graduate School of Arts and Sciences
Discipline: Biology
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Brandoli, Francesco. "Classificazione delle galassie: caratteristiche morfologiche, fotometriche e cinematiche." Bachelor's thesis, Alma Mater Studiorum - Università di Bologna, 2021. http://amslaurea.unibo.it/23934/.
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In questa tesi viene presentata la classificazione delle galassie basata su caratteristiche morfologiche, fotometriche e cinematiche. L'elaborato è articolato in tre sezioni. Nella prima è stata presentata la prima classificazione proposta da Edwin Hubble con una breve analisi delle componenti e dei meccanismi di formazione stellare (responsabili della forma macroscopica degli oggetti studiati) in maniera tale da avere una prima idea sulle forme possibili di questi oggetti e da cosa siano composti. Nella seconda vengono presentati gli osservabili che caratterizzano l'analisi fotometrica e le diverse relazioni empiriche che approfondiscono la catalogazione e le caratteristiche morfologiche non direttamente osservabili (i.e. legge di de Vaucouleurs, legge di Faber-Jackson, legge di Kormendy, relazione $D_n$ - $\sigma$ e legge di Freeman). La terza ed ultima parte è dedicata all' introduzione di elementi di statistica legati alla cinematica per un sistema di n-corpi libero di evolvere nello spazio e nel tempo, una veloce analisi dei sistemi non collisionali legata alla forma delle galassie ellittiche ed alla descrizione teorica ed empirica della curva di rotazione delle galassie a spirale che portò alla teorizzazione dell'esistenza della materia oscura.
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Keshri, Vivek. "Evolutionary analysis of the β-lactamase families." Thesis, Aix-Marseille, 2018. http://www.theses.fr/2018AIXM0250.
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Les antibiotiques β-lactamines sont parmi les médicaments antimicrobiens les plus anciens et les plus utilisés. L'enzyme bactérienne β-lactamase hydrolyse l'antibiotique β-lactame en cassant la structure de base "anneau β-lactame". Pour identifier les nouvelles β-lactamases, une étude complète a été réalisée dans diverses bases de données biologiques telles que Human Microbiome Project, env_nr et NCBI nr. L'analyse a révélé que les séquences ancestrales putatives et les recherches de profil HMM jouaient un rôle important dans l'identification de la base de données homologue et métagénomique à distance dans l'enzyme β-lactamase existante comme matière noire. Les larges analyses phylogénétiques des β-lactamases existantes et nouvellement identifiées représentent les nouveaux clades dans les arbres. En outre, l'activité d'hydrolyse des antibiotiques β-lactamines de séquences nouvellement identifiées (provenant d'archées et d'humains) a été étudiée en laboratoire, ce qui montre l'activité de la β-lactamase. La deuxième phase de l'étude a été entreprise pour examiner l'évolution fonctionnelle des β-lactamases. Premièrement, des séquences de protéines ß-lactamase 1155 ont été extraites de la base de données ARG-ANNOT et des valeurs CMI la littérature correspondante. Les résultats ont révélé que l'activité fonctionnelle de la β-lactamase évoluait de manière convergente au sein de la classe moléculaire. La troisième phase de cette thèse représente le développement d'une base de données intégrative de β-lactamases. La base de données publique actuelle de β-lactamases a des informations limitées, par conséquence, une base de données intégrative a été développéeThe β-lactam antibiotics are one of the oldest and widely used antimicrobial drugs. The bacterial enzyme β-lactamase hydrolyzes the β-lactam antibiotic by breaking the core structure “β-lactam ring”. To identify the novel β-lactamases a comprehensive investigation was performed in different biological databases such as Human Microbiome Project, env_nr, and NCBI nr. The analysis revealed that putative ancestral sequences and HMM profile searches played a significant role in the identification of remote homologous and uncovered the existing β-lactamase enzyme in the metagenomic database as dark-matter. The comprehensive phylogenetic analyses of extant and newly identified β-lactamase represent the novel clades in the trees. Further, the β-lactam antibiotic hydrolysis activity of newly identified sequences (from archaea and human) was investigated in laboratory, which shows β-lactamase activity.The second phase of the investigation was undertaken to examine the functional evolution of β-lactamases. First, 1155 β-lactamase protein sequences were retrieved from ARG-ANNOT database and MIC values from the corresponding literature. The results revealed that the functional activity of β-lactamase evolved convergently within the molecular class.The third phase of this thesis presents development of an integrative β-lactamase database. The existing public database of β-lactamase has limited information, therefore, an integrative database was developed
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Debeljak, Pavla. "The coupling of carbon and iron cycles in the Southern Ocean through microbial metabolism." Electronic Thesis or Diss., Sorbonne université, 2019. https://accesdistant.sorbonne-universite.fr/login?url=https://theses-intra.sorbonne-universite.fr/2019SORUS194.pdf.
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L'océan Austral est caractérisé par l’acronyme anglais (HNLC) signifiant qu’il contient des concentrations en nutriments élevées, mais que la biomasse phytoplanctonique y est faible. Cette situation paradoxale est due à la limitation du phytoplancton par le fer (Fe). L'augmentation de la biomasse phytoplanctonique en réponse à l'apport de Fe et, par conséquent, une plus grande absorption de dioxyde de carbone (CO2), a été démontrée dans plusieurs expériences de fertilisation artificielle et dans des régions naturellement fertilisées de l'océan Austral. Cependant, l'impact de Fe sur les procaryotes marins, acteurs clés du cycle du carbone marin, reste mal compris. En plus du Fe, les concentrations de carbone organique dissous (COD) sont faibles dans les eaux de surface de l'océan Austral, ce qui entraîne une double limitation pour l’activité et de la croissance des procaryotes hétérotrophes. Pour mieux comprendre le rôle des différents taxons procaryotes dans les cycles de Fe et de C, plusieurs aspects ont été pris en compte dans la thèse actuelle. Les résultats présentés dans cette thèse fournissent de nouvelles perspectives sur le lien entre les divers taxons microbiens et leur rôle dans le cycle du Fe- et du C dans l'océan AustralThe Southern Ocean is known as a High Nutrient Low Chlorophyll (HNLC) region where major nutrients are present at high concentrations, but phytoplankton biomass remains low. This paradoxical situation is due to iron (Fe) limitation of phytoplankton growth. The increase in phytoplankton biomass in response to Fe input and the consequently higher uptake of carbon dioxide (CO2) were demonstrated in several artificial fertilization experiments and in naturally fertilized regions of the Southern Ocean. However, the impact of Fe on marine prokaryotes, key players in the marine carbon cycle, remains poorly understood. In addition to Fe, concentrations of dissolved organic carbon (DOC) are low in surface waters of the Southern Ocean, leading to a double constraint of microbial heterotrophic activity and growth. To better understand the role of different prokaryotic taxa in the Fe- and C-cycles, several aspects were considered in the present thesis. The results presented in this thesis provide novel insights on the link between diverse microbial taxa and their role in the Fe- and C-cycling in the Southern Ocean
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Beka, Sylvia Enobong. "The genomics of Type 1 Diabetes susceptibility regions and effect of regulatory SNPs." Thesis, University of Hertfordshire, 2016. http://hdl.handle.net/2299/17200.
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Human complex diseases, like Diabetes and Cancer, affect many people worldwide today. Despite existing knowledge, many of these diseases are still not preventable. Complex diseases are known to be caused by a combination of genetic factors, as well as environmental and life style factors. The scope of this investigation covered the genomics of Type 1 Diabetes (T1D). There are 49 human genomic regions that are known to carry markers (disease-associated single nucleotide mutations) for T1D, and these were extensively studied in this research. The aim was to find out in how far this disease may be caused by problems in gene regulation rather than in gene coding. For this, the genetic factors associated with T1D, including the single point mutations and susceptibility regions, were characterised on the basis of their genomic attributes. Furthermore, mutations that occur in binding sites for transcription factors were analysed for change in the conspicuousness of their binding region, caused by allele substitution. This is called SNP (Single nucleotide polymorphism) sensitivity. From this study, it was found that the markers for T1D are mostly non-coding SNPs that occur in introns and non-coding gene transcripts, these are structures known to be involved in gene regulatory activity. It was also discovered that the T1D susceptibility regions contain an abundance of intronic, non-coding transcript and regulatory nucleotides, and that they can be split into three distinct groups on the basis of their structural and functional genomic contents. Finally, using an algorithm designed for this study, thirty-seven SNPs that change the representation of their surrounding region were identified. These regulatory mutations are non-associated T1D-SNPs that are mostly characterised by Cytosine to Thymine (C-T) transition mutations. They were found to be closer in average distance to the disease-associated SNPs than other SNPs in binding sites, and also to occur frequently in the binding motifs for the USF (Upstream stimulatory factor) protein family which is linked to problems in Type 2 diabetes.
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Lin, Yu-Cheng, and 林昱呈. "Whole Genome Phylogeny of Prokaryotes by Unique Sequence Profiles: A Rapid Alignment-free Approach." Thesis, 2015. http://ndltd.ncl.edu.tw/handle/jwqwqa.
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碩士長榮大學
生物科技學系(所)
103
Traditional methods for bacterial phylogeny are mostly constructed based on the variations from a few conserved genes. However, the variations of these conserved genes among evolutionary close species or strains are generally indistinguishable or even none. Therefore, it is almost impossible to draw any phylogenetic conclusion for very close species using conserved genes approach. Thanks to the increasing amount of completed bacterial genomes, much recent attention has turned to the application of whole genome for bacterial phylogeny. Many computational tools have been created for whole genome phylogeny. These tools are frequently being categorized as alignment or alignment-free whole genome phylogeny depending on whether or not the sequence comparison procedure being used. For the concurrent exhaustive calculation of large amount of genome sequence information, the existing methods tend to be time-consuming and have to rely on extensive computing power. This project aims at developing a rapid alignment-free whole genome phylogeny method for prokaryotes by using the unique string profiles. The method makes whole genome phylogeny by using only small amount of representative unique sequences from each genome. Without the need of counting large amount of redundant sequences frequencies existing in previous tools, it can be more efficiently handle the rapidly increasing number of bacterial genomes. This tool requires low computing power and all the programs can be installed in a desktop PC running on LINUX system.
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Yasin, Layal. ""Multiple Sequence Alignment Using External Sources Of Information"." Doctoral thesis, 2016. http://hdl.handle.net/11858/00-1735-0000-0028-870E-7.
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劉力彰. "Detection of remote homologues by sequence profile-profile comparison." Thesis, 2005. http://ndltd.ncl.edu.tw/handle/87186673501531121083.
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Chao, Tung-Fang. "Disulfide Connectivity Prediction using Sequence Distance Profile." 2004. http://www.cetd.com.tw/ec/thesisdetail.aspx?etdun=U0001-1807200423563300.
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Chao, Tung-Fang, and 趙東方. "Disulfide Connectivity Prediction using Sequence Distance Profile." Thesis, 2004. http://ndltd.ncl.edu.tw/handle/77111864404030889829.
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碩士國立臺灣大學
資訊工程學研究所
92
Motivation. Disulfide bonds play an important role in protein folding. The exact prediction of disulfide connectivity can reduce the search space in protein structure prediction. Therefore, the exact prediction of the disulfide connectivity may help the 3D structure prediction. Result. In this paper, we proposed a simple rule to define a disulfide connectivity pattern. “The same disulfide connectivity patterns have the same distance between two cysteines in protein sequences.” We used this rule to create a disulfide profile, and then used a minimum distance scoring function to predict disulfide connectivity. We reported the experimental results in two test sets. The first test set is to compare our method with other algorithms. The second test set is to test the performance for unknown protein. In the first experiment, the value of Qp is equal to 0.49 for non-redundant proteins in test set with less than 30% sequence identity. This result is better than the other algorithms (Qp=0.44). In the second experiment, the value of Qp is equal to 0.53 for non-redundant proteins in test set with less than 30% sequence identity. Therefore, we believe that using our disulfide profile, we can achieve high accuracy in predicting unknown protein. The method proposed here is relatively simple and can generate more accurate results than conventional methods. It may also be combined with other algorithms for further improvements in disulfide connectivity prediction.
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Wang, Chih-Yuan, and 王志淵. "RDHSP-Recognize Distant Homologues by Sequence-structure Profile alignment." Thesis, 2004. http://ndltd.ncl.edu.tw/handle/hq6986.
Full textAbstract:
碩士國立交通大學
生物資訊研究所
92
The RDHSP (Recognize Distant Homologues by Sequence-struc- ture Profile com- parison) is the protein fold recognition using the threading method. For a given target protein seq- uence and a template structure, RDHSP guarantees to find a globally optimal threading alignment between the two. RDHSP is based upon the premise that structure is better conserv- ed than sequence. Every residue in a protein tertiary stru- cture exists in a particular environment that can be descr- ibed by features such as main-chain conform- ation, solvent accessibility, and contact energy, contact residue numbers. RDHSP empl- oys environment-specific scoring table that of- fer a more precise and discriminating measure of substitut- ion probabilities. Compare with the popular PSI-BLAST, RDHSP is 4.6%, 22.2% and 21.6% more sensitive in detecting the family, superfamily, fold simila- rities in the Lindal benchmark.
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Tseng, Shih-Wei, and 曾世維. "Prediction of the Phosphorylation Sites in Protein Sequences Using Profile Hidden Markov Model." Thesis, 2004. http://ndltd.ncl.edu.tw/handle/70791115907793823983.
Full textAbstract:
碩士國立中央大學
生命科學研究所
92
The phosphorylation of proteins, which is an important mechanism in post-translational modification, affects essentially cellular process such as metabolism, cell signaling, differentiation and membrane transportation. Phosphorylation is performed by protein kinases. The aim here is to computationally predict phosphorylation sites within given protein sequences. The known phosphorylation sites are categorized by substrate sequences and their corresponding protein kinase classes. Profile Hidden Markov Model (HMM) is applied for learning to each group of sequences surrounding to the phosphorylation residues. A predictive tool of protein phosphorylation sites, namely KinasePhos, is implemented to allow users submit protein sequences for prediction of phosphorylation sites. By comparing to other approaches previously developed, our method has higher accuracy and provides not only the location of the phosphorylation sites, but also the corresponding catalytic protein kinases.
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Lee, Ying-Chun, and 李英準. "Detection of LTR Structures in Human Genomic Sequences Using Profile Hidden Markov Models." Thesis, 2004. http://ndltd.ncl.edu.tw/handle/33134356623923404368.
Full textAbstract:
碩士國立中央大學
資訊工程研究所
92
More then 45% of human genome was annotated as transposable elements (TEs). The expansion of the human genome is resulted from the mobilization of these TEs and they may increase the plasticity and variation in our genome. Long terminal repeat (LTR) retrotransposons are major components in TEs. There are regulatory sites in LTR and we believe that they could be conserved in evolution. Therefore, we search for these significant motifs in the sequence of LTRs and these motifs are used to train Hidden Markov Model (HMM). Using these models as fingerprints, we can detect most of the known LTRs detected by RepeatMasker and LTR instances are classified into families using the predictive models proposed. It could be helpful for evolution analysis.
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"Epidemiological risk profile of human papillomavirus type 52 infection and its sequence diversity among the general population and cervical cancer patients in Hong Kong." 2007. http://library.cuhk.edu.hk/record=b5893412.
Full textAbstract:
Ho, Ching Sze.Thesis (M.Phil.)--Chinese University of Hong Kong, 2007.
Includes bibliographical references (leaves 142-160).
Abstracts in English and Chinese.
DECLARATION --- p.I
ACKNOWLEDGEMENTS --- p.II
ABSTRACT (ENGLISH VERSION) --- p.IV
ABSTRACT (CHINESE VERSION) --- p.VII
TABLE OF CONTENTS --- p.IX
LIST OF FUGURES --- p.XII
LIST OF TABLES --- p.XIII
LIST OF ABBREVIATIONS --- p.XV
Chapter CHAPTER 1: --- INTRODUCTION --- p.1
Chapter 1.1 --- Biology of human papillomavirus --- p.2
Chapter 1.1.1 --- History --- p.2
Chapter 1.1.2 --- Classification --- p.3
Chapter 1.1.3 --- Genome structure --- p.5
Chapter 1.1.4 --- Life cycle --- p.9
Chapter 1.2 --- Epidemiology of cervical cancer --- p.10
Chapter 1.2.1 --- Cervical intraepithelial neoplasia and cervical cancer --- p.10
Chapter 1.2.2 --- Spectrum of cervical neoplasia --- p.13
Chapter 1.2.3 --- Incidence of cervical cancer --- p.15
Chapter 1.2.4 --- Screening programme --- p.16
Chapter 1.3 --- Risk factors for cervical cancer --- p.17
Chapter 1.4 --- Oncogenic HPV infection --- p.20
Chapter 1.4.1 --- Risk association --- p.21
Chapter 1.4.2 --- Geographical distribution --- p.23
Chapter 1.4.3 --- Age distribution --- p.24
Chapter 1.4.4 --- Oncogenic property of HPV --- p.25
Chapter 1.4.5 --- Sequence variation --- p.28
Chapter 1.5 --- Prevention by vaccination --- p.30
Chapter 1.6 --- Objectives --- p.31
Chapter CHAPTER 2: --- MATERIALS AND METHODS --- p.33
Chapter 2.1 --- HPV type and prevalence distribution --- p.34
Chapter 2.1.1 --- Study population --- p.34
Chapter 2.1.2 --- Specimen and epidemiological data collection --- p.34
Chapter 2.1.3 --- DNA extraction --- p.35
Chapter 2.1.4 --- PCR amplification of DNA --- p.36
Chapter 2.1.4.1 --- PCR for Beta-globin --- p.36
Chapter 2.1.4.2 --- PCR for HPV DNA --- p.37
Chapter 2.1.5 --- HPV typing by reverse line-blot hybridization --- p.39
Chapter 2.1.6 --- Statistical method --- p.40
Chapter 2.2 --- HPV 52 SEQUENCE VARIATION --- p.43
Chapter 2.2.1 --- Study population --- p.43
Chapter 2.2.2 --- Specimen processing --- p.43
Chapter 2.2.3 --- DNA extraction --- p.44
Chapter 2.2.4 --- PCR amplification for sequencing --- p.45
Chapter 2.2.4.1 --- Optimization of gene-specific PCR --- p.45
Chapter 2.2.4.2 --- Validation of type-specificity of gene-specific PCR --- p.46
Chapter 2.2.4.3 --- PCR for HPV52 E6 and E7 --- p.46
Chapter 2.2.4.4 --- PCR for LI gene --- p.47
Chapter 2.2.4.5 --- PCR for long control region (LCR) --- p.48
Chapter 2.2.5 --- Purification of PCR products --- p.49
Chapter 2.2.6 --- Sequencing --- p.50
Chapter 2.2.6.1 --- Preparation of template --- p.50
Chapter 2.2.6.2 --- Purification of template --- p.50
Chapter 2.2.6.3 --- Sequencer and data analysis --- p.51
Chapter 2.2.7 --- Statistical methods --- p.51
Chapter CHAPTER 3: --- RESULTS --- p.54
Chapter 3.1 --- HPV TYPE AND PREVALENCE DISTRIBUTION --- p.55
Chapter 3.1.1 --- Study population --- p.55
Chapter 3.1.2 --- HPV prevalence --- p.59
Chapter 3.1.2.1 --- Prevalence for HPV infection --- p.59
Chapter 3.1.2.2 --- HPV age-specific prevalence --- p.68
Chapter 3.1.3 --- Epidemiological risk profile --- p.73
Chapter 3.1.3.1 --- Age-adjusted analyses --- p.73
Chapter 3.1.3.2 --- Multivariate analyses --- p.76
Chapter 3.2 --- HPV52 SEQUENCE VARIATION --- p.79
Chapter 3.2.1 --- Study population --- p.79
Chapter 3.2.2 --- Sequence variability of HPV52 --- p.79
Chapter 3.2.3 --- HPV52 --- p.82
Chapter 3.2.3.1 --- Sequence variation of E6 ORF --- p.82
Chapter 3.2.3.2. --- HPV52 E6 variants and risk for cervical neoplasia --- p.86
Chapter 3.2.4 --- HPV52 E7 --- p.89
Chapter 3.2.4.1 --- Sequence variation of E7 ORF --- p.89
Chapter 3.2.4.2 --- HPV52 E7 variants and risk for cervical neoplasia --- p.93
Chapter 3.2.5 --- HPV52 LI --- p.95
Chapter 3.2.5.1 --- Sequence variation of LI ORF --- p.95
Chapter 3.2.5.2 --- HPV52 LI variants and risk for cervical neoplasia --- p.100
Chapter 3.2.6 --- HPV52 long control region (LCR) --- p.104
Chapter 3.2.6.1 --- Sequence variation of LCR --- p.104
Chapter 3.2.6.2 --- HPV52 LCR variants and risk for cervical neoplasia --- p.110
Chapter CHAPTER 4: --- DISCUSSION --- p.113
Chapter 4.1 --- HPV PREVALENCE AND TYPE DISTRIBUTION --- p.114
Chapter 4.1.1 --- HPV prevalence --- p.114
Chapter 4.1.2 --- Age-specific prevalence --- p.116
Chapter 4.1.3 --- Epidemiological risk profile --- p.121
Chapter 4.1.4 --- Conclusions --- p.126
Chapter 4.2 --- HPV 52 SEQUENCE VARIATION --- p.127
Chapter 4.2.1 --- Sequence variability of HPV52 --- p.127
Chapter 4.2.2 --- Sequence variation of E6 gene --- p.129
Chapter 4.2.3 --- Sequence variation of E7 gene --- p.132
Chapter 4.2.4 --- Sequence variation of LI gene --- p.134
Chapter 4.2.5 --- Sequence variation of LCR --- p.135
Chapter 4.2.6 --- Conclusions --- p.139
Chapter 4.3 --- FURTHER STUDIES --- p.140
REFERENCES --- p.142
APPENDIXES --- p.A
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"Seed Coat Color in Flax (Linum usitatissimum L.) Conditioned by the b1 Locus, its Linkage with Simple Sequence Repeat Markers (SSRs) and its Association with Flower Shape, Flower Color, Fatty Acid Profile and Grain Yield." Thesis, 2015. http://hdl.handle.net/10388/ETD-2015-01-1989.
Full textAbstract:
Previously seed coat color in flax has been used as a phenotypic marker for specialty quality traits and currently there is an increasing demand to use seed coat color in flax to market flax for human and animal nutrition uses. Seed coat color was studied to 1) understand the inheritance of seed coat color conditioned by the b1 locus, to 2) understand the relationship of other important flax traits with seed coat color as well as to 3) identify markers that are linked to seed coat color for future marker assisted selection of seed coat color. Spearman’s rank correlation and an allelism test was used to show the inheritance of the alleles at the b1 locus. Bulked segregant analysis (BSA) was used to identify putatively linked markers with the b1 locus, these were then screened on the CDC Bethune x M96006 recombinant inbred line population. Furthermore, the CDC Bethune x M96006 and CDC Bethune x USDA-ARS Crystal recombinant inbred line populations were used to identify any important flax traits that had a significant relationship with seed coat color. It was shown that seed coat color conditioned by the b1 locus was stably inherited and that b1vg and b1 are allelic to one another. The results of the BSA showed that there were 17 candidates for linkage but when these markers were screened on the population only the Lu456 from linkage group (LG) six was identified to have linkage (χ²=3.90; P<0.05) with the b1 locus. Additionally, it was shown that the b1 seed coat color allele of the b1 locus had a pleiotropic effect on flower color and flower shape and that seed coat color was associated with linolenic fatty acid content. None of the traits examined were found to be associated with the b1vg allele of this locus. These results show that the b1 locus is likely present on linkage group six, more marker coverage on linkage group six of markers that are polymorphic between the two seed coat color parents would increase the accuracy of detection. Lastly, this study showed that plant breeders should consider using the b1vg allele that conditions the variegated seed coat color to mark unique lines with important combinations of traits because it sorted independently for seed quality traits. Whereas, the yellow seed coat color conditioned by the b1 allele was found to be associated with higher linolenic fatty acid content and the semi-lethality of this allele would make it not suitable for use in parental lines.
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Yadwadkar, Neeraja. "Discovery Of Application Workloads From Network File Traces." Thesis, 2009. http://hdl.handle.net/2005/1213.
Full textAbstract:
An understanding of Input/Output data access patterns of applications is useful in several situations. First, gaining an insight into what applications are doing with their data at a semantic level helps in designing efficient storage systems. Second, it helps to create benchmarks that mimic realistic application behavior closely. Third, it enables autonomic systems as the information obtained can be used to adapt the system in a closed loop.
All these use cases require the ability to extract the application-level semantics of I/O operations. Methods such as modifying application code to associate I/O operations with semantic tags are intrusive. It is well known that network file system traces are an important source of information that can be obtained non-intrusively and analyzed either online or offline. These traces are a sequence of primitive file system operations and their parameters. Simple counting, statistical analysis or deterministic search techniques are inadequate for discovering application-level semantics in the general case, because of the inherent variation and noise in realistic traces.
In this paper, we describe a trace analysis methodology based on Profile Hidden Markov Models. We show that the methodology has powerful discriminatory capabilities that enables it to recognize applications based on the patterns in the traces, and to mark out regions in a long trace that encapsulate sets of primitive operations that represent higher-level application actions. It is robust enough that it can work around discrepancies between training and target traces such as in length and interleaving with other operations. We demonstrate the feasibility of recognizing patterns based on a small sampling of the trace, enabling faster trace analysis. Preliminary experiments show that the method is capable of learning accurate profile models on live traces in an online setting. We present a detailed evaluation of this methodology in a UNIX environment using NFS traces of selected commonly used applications such as compilations as well as on industrial strength benchmarks such as TPC-C and Postmark, and discuss its capabilities and limitations in the context of the use cases mentioned above.
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Li, Zhixiu. "Computational protein design: assessment and applications." Thesis, 2015. http://hdl.handle.net/1805/7949.
Full textAbstract:
Indiana University-Purdue University Indianapolis (IUPUI)Computational protein design aims at designing amino acid sequences that can fold into a target structure and perform a desired function. Many computational design methods have been developed and their applications have been successful during past two decades. However, the success rate of protein design remains too low to be of a useful tool by biochemists whom are not an expert of computational biology. In this dissertation, we first developed novel computational assessment techniques to assess several state-of-the-art computational techniques. We found that significant progresses were made in several important measures by two new scoring functions from RosettaDesign and from OSCAR-design, respectively. We also developed the first machine-learning technique called SPIN that predicts a sequence profile compatible to a given structure with a novel nonlocal energy-based feature. The accuracy of predicted sequences is comparable to RosettaDesign in term of sequence identity to wild type sequences. In the last two application chapters, we have designed self-inhibitory peptides of Escherichia coli methionine aminopeptidase (EcMetAP) and de novo designed barstar. Several peptides were confirmed inhibition of EcMetAP at the micromole-range 50% inhibitory concentration. Meanwhile, the assessment of designed barstar sequences indicates the improvement of OSCAR-design over RosettaDesign.
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Creighton, Graham Robert. "An assessment of student's English vocabulary levels and an exploration of the vocabulary profile of teacher's spoken discourse in an international high school." Diss., 2016. http://hdl.handle.net/10500/22590.
Full textAbstract:
In many international schools where English is the language of learning and teaching there are large percentages of students whose first language is not English. Many of these students may have low vocabulary levels which inhibits their chances of taking full advantage of their education. Low vocabulary levels can be a particular problem for students in mainstream classes where fluent English speaking teachers are using English to teach content areas of Mathematics, Science and History. Not only do students have to comprehend the low-frequency, academic and technical vocabulary pertaining to the subject, but they also need to know the higher frequency vocabulary that makes up general English usage. If students’ vocabulary levels fall too far below the vocabulary levels with which their teachers are speaking, then their chance of comprehending the topic is small, as is their chance of succeeding in their subjects.
This study has two broad aims. Firstly, I have set out to assess the English vocabulary levels of students at an international school where English is the language of learning and teaching. The majority of students at this school do not have English as their first language. The second aim of this study is to explore the vocabulary profile of the teachers’ spoken discourse at the research school. By gaining a better understanding of the nature of teacher discourse – specifically the percentage of high, mid and low-frequency vocabulary, as well as academic vocabulary that they use – English as a Second Language (ESL) teachers will be in a stronger position to identify what the vocabulary learning task is and be able to assist students in reaching the vocabulary levels necessary to make sense of their lessons. This study revealed a large gap between the generally low vocabulary levels of ESL students and the vocabulary levels spoken by their teachers. As a result the need for explicit vocabulary instruction and learning is shown to be very important in English medium (international) schools, where there are large numbers of students whose first language is not English.Linguistics and Modern Languages
M.A. (Applied Linguistics)