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Relevant bibliographies by topics / Sequence alignment Sequence analysis / Dissertations / Theses

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Dissertations / Theses on the topic 'Sequence alignment Sequence analysis'

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Published: 4 June 2021

Last updated: 9 February 2022

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1

Starrett, Dean. "Optimal Alignment of Multiple Sequence Alignments." Diss., The University of Arizona, 2008. http://hdl.handle.net/10150/194840.

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An essential tool in biology is the alignment of multiple sequences. Biologists use multiple sequence alignments for tasks such as predicting protein structure and function, reconstructing phylogenetic trees, and finding motifs. Constructing high-quality multiple alignments is computationally hard, both in theory and in practice, and is typically done using heuristic methods. The majority of state-of-the-art multiple alignment programs employ a form and polish strategy, where in the construction phase, an initial multiple alignment is formed by progressively merging smaller alignments, startin

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2

Powell, David Richard 1973. "Algorithms for sequence alignment." Monash University, School of Computer Science and Software Engineering, 2001. http://arrow.monash.edu.au/hdl/1959.1/8051.

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3

Ho, Ngai-lam, and 何毅林. "Algorithms on constrained sequence alignment." Thesis, The University of Hong Kong (Pokfulam, Hong Kong), 2004. http://hub.hku.hk/bib/B30201949.

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4

Arner, Erik. "Solving repeat problems in shotgun sequencing /." Stockholm, 2006. http://diss.kib.ki.se/2006/91-7140-996-3/.

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5

Rausch, Tobias [Verfasser]. "Dissecting multiple sequence alignment methods : the analysis, design and development of generic multiple sequence alignment components in SeqAn / Tobias Rausch." Berlin : Freie Universität Berlin, 2010. http://d-nb.info/1024541460/34.

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6

Kim, Eagu. "Inverse Parametric Alignment for Accurate Biological Sequence Comparison." Diss., The University of Arizona, 2008. http://hdl.handle.net/10150/193664.

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For as long as biologists have been computing alignments of sequences, the question of what values to use for scoring substitutions and gaps has persisted. In practice, substitution scores are usually chosen by convention, and gap penalties are often found by trial and error. In contrast, a rigorous way to determine parameter values that are appropriate for aligning biological sequences is by solving the problem of Inverse Parametric Sequence Alignment. Given examples of biologically correct reference alignments, this is the problem of finding parameter values that make the examples score as

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7

Maydt, Jochen. "Analysis of recombination in molecular sequence data." Aachen Shaker, 2008. http://d-nb.info/993318045/04.

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8

Herman, Joseph L. "Multiple sequence analysis in the presence of alignment uncertainty." Thesis, University of Oxford, 2014. http://ora.ox.ac.uk/objects/uuid:88a56d9f-a96e-48e3-b8dc-a73f3efc8472.

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Sequence alignment is one of the most intensely studied problems in bioinformatics, and is an important step in a wide range of analyses. An issue that has gained much attention in recent years is the fact that downstream analyses are often highly sensitive to the specific choice of alignment. One way to address this is to jointly sample alignments along with other parameters of interest. In order to extend the range of applicability of this approach, the first chapter of this thesis introduces a probabilistic evolutionary model for protein structures on a phylogenetic tree; since protein stru

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9

Bell, Lachlan Hamilton. "Sequence analysis of enzymes of the shikimate pathway : development of a novel multiple sequence alignment algorithm." Thesis, University of Glasgow, 1996. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.307193.

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10

Hossain, A. S. Md Mukarram. "Scalable tools for high-throughput viral sequence analysis." Thesis, University of Cambridge, 2017. https://www.repository.cam.ac.uk/handle/1810/276228.

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Viral sequence data are increasingly being used to estimate evolutionary and epidemiological parameters to understand the dynamics of viral diseases. This thesis focuses on developing novel and improved computational methods for high-throughput analysis of large viral sequence datasets. I have developed a novel computational pipeline, Pipelign, to detect potentially unrelated sequences from groups of viral sequences during sequence alignment. Pipelign detected a large number of unrelated and mis-annotated sequences from several viral sequence datasets collected from GenBank. I subsequently dev

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11

Gupta, Kapil. "Combinatorial optimization and application to DNA sequence analysis." Diss., Atlanta, Ga. : Georgia Institute of Technology, 2008. http://hdl.handle.net/1853/26676.

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Thesis (Ph.D)--Industrial and Systems Engineering, Georgia Institute of Technology, 2009.<br>Committee Chair: Lee, Eva K.; Committee Member: Barnes, Earl; Committee Member: Fan, Yuhong; Committee Member: Johnson, Ellis; Committee Member: Yuan, Ming. Part of the SMARTech Electronic Thesis and Dissertation Collection.

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12

Abhiman, Saraswathi. "Prediction of function shift in protein families /." Stockholm, 2006. http://diss.kib.ki.se/2006/91-7140-869-X/.

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13

Lassmann, Timo. "Algorithms for building and evaluating multiple sequence alignments /." Stockholm, 2006. http://diss.kib.ki.se/2006/91-7140-887-8/.

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14

Tran, Hong Thi Thanh. "Evaluating and Improving Performance of Bisulfite Short Reads Alignment and the Identification of Differentially Methylated Sites." Diss., Virginia Tech, 2018. http://hdl.handle.net/10919/81861.

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Large-scale bisulfite treatment and short reads sequencing technology allows comprehensive estimation of methylation states of Cs in the genomes of different tissues, cell types, and developmental stages. Accurate characterization of DNA methylation is essential for understanding genotype phenotype association, gene and environment interaction, diseases, and cancer. The thesis work first evaluates the performance of several commonly used bisulfite short read mappers and investigates how pre-processing data might affect the performance. Aligning bisulfite short reads to a reference genome remai

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15

Hollich, Volker. "Orthology and protein domain architecture evolution /." Stockholm, 2006. http://diss.kib.ki.se/2006/91-7140-783-9/.

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16

Larson, Stefan M. "A comprehensive sequence alignment analysis and structure comparison of the SH3 domain family." Thesis, National Library of Canada = Bibliothèque nationale du Canada, 1999. http://www.collectionscanada.ca/obj/s4/f2/dsk1/tape7/PQDD_0002/MQ46094.pdf.

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17

Lee, Marianne M. "A two-pronged approach to improve distant homology detection." Columbus, Ohio : Ohio State University, 2009. http://rave.ohiolink.edu/etdc/view?acc%5Fnum=osu1242235868.

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18

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 a

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19

Tångrot, Jeanette. "Structural Information and Hidden Markov Models for Biological Sequence Analysis." Doctoral thesis, Umeå universitet, Institutionen för datavetenskap, 2008. http://urn.kb.se/resolve?urn=urn:nbn:se:umu:diva-1629.

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Bioinformatics is a fast-developing field, which makes use of computational methods to analyse and structure biological data. An important branch of bioinformatics is structure and function prediction of proteins, which is often based on finding relationships to already characterized proteins. It is known that two proteins with very similar sequences also share the same 3D structure. However, there are many proteins with similar structures that have no clear sequence similarity, which make it difficult to find these relationships. In this thesis, two methods for annotating protein domains are

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20

Weber, Matthias. "Structural Performance Comparison of Parallel Software Applications." Doctoral thesis, Saechsische Landesbibliothek- Staats- und Universitaetsbibliothek Dresden, 2016. http://nbn-resolving.de/urn:nbn:de:bsz:14-qucosa-216133.

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With rising complexity of high performance computing systems and their parallel software, performance analysis and optimization has become essential in the development of efficient applications. The comparison of performance data is a key operation required in performance analysis. An analyst may conduct different types of comparisons in order to understand the performance properties of an application. One use case is comparing performance data from multiple measurements. Typical examples for such comparisons are before/after comparisons when applying optimizations or changing code versions. B

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21

Coco, Joseph. "PARSES: A Pipeline for Analysis of RNA-Sequencing Exogenous Sequences." ScholarWorks@UNO, 2011. http://scholarworks.uno.edu/td/1297.

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RNA-Sequencing (RNA-Seq) has become one of the most widely used techniques to interrogate the transcriptome of an organism since the advent of next generation sequencing technologies [1]. A plethora of tools have been developed to analyze and visualize the transcriptome data from RNA-Seq experiments, solving the problem of mapping reads back to the host organism's genome [2] [3]. This allows for analysis of most reads produced by the experiments, but these tools typically discard reads that do not match well with the reference genome. This additional information could reveal important insight

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22

Brand, Michael, and Mansi Gupta. "Identification and Expression Analysis of Zebrafish Glypicans during Embryonic Development." Saechsische Landesbibliothek- Staats- und Universitaetsbibliothek Dresden, 2015. http://nbn-resolving.de/urn:nbn:de:bsz:14-qucosa-185658.

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Heparan sulfate Proteoglycans (HSPG) are ubiquitous molecules with indispensable functions in various biological processes. Glypicans are a family of HSPG’s, characterized by a Gpi-anchor which directs them to the cell surface and/or extracellular matrix where they regulate growth factor signaling during development and disease. We report the identification and expression pattern of glypican genes from zebrafish. The zebrafish genome contains 10 glypican homologs, as opposed to six in mammals, which are highly conserved and are phylogenetically related to the mammalian genes. Some of the fish

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23

Brand, Michael, and Mansi Gupta. "Identification and Expression Analysis of Zebrafish Glypicans during Embryonic Development." PLoS, 2013. https://tud.qucosa.de/id/qucosa%3A29015.

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Heparan sulfate Proteoglycans (HSPG) are ubiquitous molecules with indispensable functions in various biological processes. Glypicans are a family of HSPG’s, characterized by a Gpi-anchor which directs them to the cell surface and/or extracellular matrix where they regulate growth factor signaling during development and disease. We report the identification and expression pattern of glypican genes from zebrafish. The zebrafish genome contains 10 glypican homologs, as opposed to six in mammals, which are highly conserved and are phylogenetically related to the mammalian genes. Some of the fish

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24

Iseric, Hamza. "BISER: fast characterization of segmental duplication structure in multiple genome assemblies." Thesis, Schloss Dagstuhl -- Leibniz-Zentrum für Informatik, 2021. http://hdl.handle.net/1828/13343.

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The increasing availability of high-quality genome assemblies raised interest in the characterization of genomic architecture. Major architectural elements, such as common repeats and segmental duplications (SDs), increase genome plasticity that stimulates further evolution by changing the genomic structure and inventing new genes. Optimal computation of SDs within a genome requires quadratic-time local alignment algorithms that are impractical due to the size of most genomes. Additionally, to perform evolutionary analysis, one needs to characterize SDs in multiple genomes and find relations b

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25

Capella, Gutiérrez Salvador Jesús 1985. "Analysis of multiple protein sequence alignments and phylogenetic trees in the context of phylogenomics studies." Doctoral thesis, Universitat Pompeu Fabra, 2012. http://hdl.handle.net/10803/97289.

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Phylogenomics is a biological discipline which can be understood as the intersection of the fields of genomics and evolution. Its main focuses are the analyses of genomes through the evolutionary lens and the understanding of how different organisms relate to each other. Moreover, phylogenomics allows to make accurate functional annotations of newly sequenced genomes. This discipline has grown in response to the deluge of data coming from different genome projects. To achieve their objectives, phylogenomics heavily depends on the accuracy of different methods to generate precise phyloge

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26

Yin, Zhaoming. "Enhance the understanding of whole-genome evolution by designing, accelerating and parallelizing phylogenetic algorithms." Diss., Georgia Institute of Technology, 2014. http://hdl.handle.net/1853/51875.

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The advent of new technology enhance the speed and reduce the cost for sequencing biological data. Making biological sense of this genomic data is a big challenge to the algorithm design as well as the high performance computing society. There are many problems in Bioinformatics, such as how new functional genes arise, why genes are organized into chromosomes, how species are connected through the evolutionary tree of life, or why arrangements are subject to change. Phylogenetic analyses have become essential to research on the evolutionary tree of life. It can help us to track the history of

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27

Pratas, Diogo. "Compression and analysis of genomic data." Doctoral thesis, Universidade de Aveiro, 2016. http://hdl.handle.net/10773/16286.

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Doutoramento em Informática<br>Genomic sequences are large codi ed messages describing most of the structure of all known living organisms. Since the presentation of the rst genomic sequence, a huge amount of genomics data have been generated, with diversi ed characteristics, rendering the data deluge phenomenon a serious problem in most genomics centers. As such, most of the data are discarded (when possible), while other are compressed using general purpose algorithms, often attaining modest data reduction results. Several speci c algorithms have been proposed for the compression of

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28

Brandström, Mikael. "Bioinformatic Analysis of Mutation and Selection in the Vertebrate Non-coding Genome." Doctoral thesis, Uppsala University, Department of Evolution, Genomics and Systematics, 2007. http://urn.kb.se/resolve?urn=urn:nbn:se:uu:diva-8240.

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<p>The majority of the vertebrate genome sequence is not coding for proteins. In recent years, the evolution of this noncoding fraction of the genome has gained interest. These studies have been greatly facilitated by the availability of full genome sequences. The aim of this thesis is to study evolution of the noncoding vertebrate genome through bioinformatic analysis of large-scale genomic datasets.</p><p>In a first analysis we addressed the use of conservation of sequence between highly diverged genomes to infer function. We provided evidence for a turnover of the patterns of negative selec

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29

Ding, Guoxiang. "DERIVING ACTIVITY PATTERNS FROM INDIVIDUAL TRAVEL DIARY DATA: A SPATIOTEMPORAL DATA MINING APPROACH." The Ohio State University, 2009. http://rave.ohiolink.edu/etdc/view?acc_num=osu1236777859.

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30

Cunial, Fabio. "Analysis of the subsequence composition of biosequences." Diss., Georgia Institute of Technology, 2012. http://hdl.handle.net/1853/44716.

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Measuring the amount of information and of shared information in biological strings, as well as relating information to structure, function and evolution, are fundamental computational problems in the post-genomic era. Classical analyses of the information content of biosequences are grounded in Shannon's statistical telecommunication theory, while the recent focus is on suitable specializations of the notions introduced by Kolmogorov, Chaitin and Solomonoff, based on data compression and compositional redundancy. Symmetrically, classical estimates of mutual information based on string editing

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31

Chia, Nicholas Lee-Ping. "Sequence alignment." Columbus, Ohio : Ohio State University, 2006. http://rave.ohiolink.edu/etdc/view?acc%5Fnum=osu1154616122.

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32

Santos-Ciminera, Patricia Dantas Ciminera Patricia Dantas Santos Santos Patricia. "Molecular epidemiology of epidemic severe malaria caused by Plasmodium vivax in the state of Amazonas, Brazil /." Download the dissertation in PDF, 2005. http://www.lrc.usuhs.mil/dissertations/pdf/Santos2005.pdf.

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33

Al, Ghamdi Manal. "Video sequence alignment." Thesis, University of Sheffield, 2015. http://etheses.whiterose.ac.uk/9056/.

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The task of aligning multiple audio visual sequences with similar contents needs careful synchronisation in both spatial and temporal domains. It is a challenging task due to a broad range of contents variations, background clutter, occlusions, and other factors. This thesis is concerned with aligning video contents by characterising the spatial and temporal information embedded in the high-dimensional space. To that end a three- stage framework is developed, involving space-time representation of video clips with local linear coding, followed by their alignment in the manifold embedded space.

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34

Cao, Haibo. "Protein Structure Recognition From Eigenvector Analysis to Structural Threading Method." Washington, D.C. : Oak Ridge, Tenn. : United States. Dept. of Energy. Office of Science ; distributed by the Office of Scientific and Technical Information, U.S. Dept. of Energy, 2003. http://www.osti.gov/servlets/purl/822060-2L2Xvm/native/.

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Thesis (Ph.D.); Submitted to Iowa State Univ., Ames, IA (US); 12 Dec 2003.<br>Published through the Information Bridge: DOE Scientific and Technical Information. "IS-T 2028" Haibo Cao. 12/12/2003. Report is also available in paper and microfiche from NTIS.

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35

Sammeth, Michael. "Integrated multiple sequence alignment." [S.l.] : [s.n.], 2005. http://deposit.ddb.de/cgi-bin/dokserv?idn=98148767X.

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36

Birney, Ewan. "Sequence alignment in bioinformatics." Thesis, University of Cambridge, 2000. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.621653.

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37

Arvestad, Lars. "Algorithms for biological sequence alignment." Doctoral thesis, KTH, Numerisk analys och datalogi, NADA, 1999. http://urn.kb.se/resolve?urn=urn:nbn:se:kth:diva-2905.

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38

Fleissner, Roland. "Sequence alignment and phylogenetic inference." Berlin : Logos Verlag, 2004. http://diss.ub.uni-duesseldorf.de/ebib/diss/file?dissid=769.

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39

Fleissner, Roland. "Sequence alignment and phylogenetic inference." [S.l. : s.n.], 2003. http://deposit.ddb.de/cgi-bin/dokserv?idn=971844704.

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40

Auer, Jens. "Metaheuristic Multiple Sequence Alignment Optimisation." Thesis, University of Skövde, School of Humanities and Informatics, 2004. http://urn.kb.se/resolve?urn=urn:nbn:se:his:diva-899.

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<p>The ability to tackle NP-hard problems has been greatly extended by the introduction of Metaheuristics (see Blum & Roli (2003)) for a summary of most Metaheuristics, general problem-independent optimisation algorithms extending the hill-climbing local search approach to escape local minima. One of these algorithms is Iterated Local Search (ILS) (Lourenco et al., 2002; Stützle, 1999a, p. 25ff), a recent easy to implement but powerful algorithm with results comparable or superior to other state-of-the-art methods for many combinatorial optimisation problems, among them the Traveling Salesman

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41

Carroll, Hyrum D. "Biologically Relevant Multiple Sequence Alignment." Diss., CLICK HERE for online access, 2008. http://contentdm.lib.byu.edu/ETD/image/etd2623.pdf.

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42

Grossmann, Steffen. "Statistics of optimal sequence alignments." [S.l. : s.n.], 2003. http://deposit.ddb.de/cgi-bin/dokserv?idn=968907466.

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43

Alimehr, Leila. "The Performance of Sequence Alignment Algorithms." Thesis, Uppsala universitet, Institutionen för informationsteknologi, 2013. http://urn.kb.se/resolve?urn=urn:nbn:se:uu:diva-200289.

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This thesis deals with sequence alignment algorithms. The sequence alignment is a mutual arrange of two or more sequences in order to study their similarity and dissimilarity. Four decades after the seminal work by Needleman and Wunsch in 1970, these methods still need more explorations. We start out with a review of a sequence alignment, and its generalization to multiple alignments, although the focus of this thesis is on the evaluation of the new alignment algorithms. The research presented here in has stepped into the different algorithms that are in terms of the dynamic programming. In th

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Jiang, Tianwei. "Sequence alignment : algorithm development and applications /." View abstract or full-text, 2009. http://library.ust.hk/cgi/db/thesis.pl?ECED%202009%20JIANG.

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45

Zhao, Kaiyong. "GPU accelerated sequence alignment /Zhao Kaiyong." HKBU Institutional Repository, 2016. https://repository.hkbu.edu.hk/etd_oa/378.

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DNA sequence alignment is a fundamental task in gene information processing, which is about searching the location of a string (usually based on newly collected DNA data) in the existing huge DNA sequence databases. Due to the huge amount of newly generated DNA data and the complexity of approximate string match, sequence alignment becomes a time-consuming process. Hence how to reduce the alignment time becomes a significant research problem. Some algorithms of string alignment based on HASH comparison, suffix array and BWT, which have been proposed for DNA sequence alignment. Although these a

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46

Löytynoja, Ari. "Molecular sequence alignment and character homology." Doctoral thesis, Universite Libre de Bruxelles, 2003. http://hdl.handle.net/2013/ULB-DIPOT:oai:dipot.ulb.ac.be:2013/211261.

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47

Zola, Jaroslaw. "Parallel server for multiple sequence alignment." Grenoble INPG, 2005. http://www.theses.fr/2005INPG0187.

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Dans ce travail réalisé au cours du Doctorat, nous nous proposons d'étudier des techniques du calcul parallèle (en particulier, les caches web) pour optimiser l'alignement multiple de séquences. Nous développons une méthode générique pour gérer un cache local ou distribué et nous présentons un système de cache décentralisé gardant en mémoire les résultats intermédiaires ainsi que les alignements de séquences. Enfin, nous construisons un serveur parallèle utilisant les techniques précédentes permettant d'aligner plus rapidement des ensembles de séquences de grandes tailles (des milliers de séqu

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48

Gîrdea, Marta. "New methods for biological sequence alignment." Thesis, Lille 1, 2010. http://www.theses.fr/2010LIL10089/document.

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L'alignement de séquences biologiques est une technique fondamentale en bioinformatique, et consiste à identifier des séries de caractères similaires (conservés) qui apparaissent dans le même ordre dans les deux séquences, et à inférer un ensemble de modifications (substitutions, insertions et suppressions) impliquées dans la transformation d'une séquence en l'autre. Cette technique permet de déduire, sur la base de la similarité de séquence, si deux ou plusieurs séquences biologiques sont potentiellement homologues, donc si elles partagent un ancêtre commun, permettant ainsi de mieux comprend

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49

DeBlasio, Daniel Frank. "Parameter Advising for Multiple Sequence Alignment." Diss., The University of Arizona, 2016. http://hdl.handle.net/10150/612932.

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The problem of aligning multiple protein sequences is essential to many biological analyses, but most standard formulations of the problem are NP-complete. Due to both the difficulty of the problem and its practical importance, there are many heuristic multiple sequence aligners that a researcher has at their disposal. A basic issue that frequently arises is that each of these alignment tools has a multitude of parameters that must be set, and which greatly affect the quality of the alignment produced. Most users rely on the default parameter setting that comes with the aligner, which is optim

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Guasco, Luciano M. "Multiple sequence alignment correction using constraints." Master's thesis, Faculdade de Ciências e Tecnologia, 2010. http://hdl.handle.net/10362/5143.

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Trabalho apresentado no âmbito do European Master in Computational Logics, como requisito parcial para obtenção do grau de Mestre em Computational Logics<br>One of the most important fields in bioinformatics has been the study of protein sequence alignments. The study of homologous proteins, related by evolution, shows the conservation of many amino acids because of their functional and structural importance. One particular relationship between the amino acid sites in the same sequence or between different sequences, is protein-coevolution, interest in which has increased as a consequen

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