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Dissertations / Theses on the topic 'Sequence alignment'

Author: Grafiati

Published: 4 June 2021

Last updated: 25 July 2025

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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

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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3

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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4

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

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5

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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6

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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7

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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8

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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9

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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10

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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11

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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12

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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13

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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14

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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15

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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16

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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17

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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18

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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19

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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20

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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21

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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22

Isa, Mohammad Nazrin. "High performance reconfigurable architectures for biological sequence alignment." Thesis, University of Edinburgh, 2013. http://hdl.handle.net/1842/7721.

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Bioinformatics and computational biology (BCB) is a rapidly developing multidisciplinary field which encompasses a wide range of domains, including genomic sequence alignments. It is a fundamental tool in molecular biology in searching for homology between sequences. Sequence alignments are currently gaining close attention due to their great impact on the quality aspects of life such as facilitating early disease diagnosis, identifying the characteristics of a newly discovered sequence, and drug engineering. With the vast growth of genomic data, searching for a sequence homology over huge dat

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23

Nguyen, Ken D. "Multiple Biolgical Sequence Alignment: Scoring Functions, Algorithms, and Evaluations." Digital Archive @ GSU, 2011. http://digitalarchive.gsu.edu/cs_diss/62.

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Aligning multiple biological sequences such as protein sequences or DNA/RNA sequences is a fundamental task in bioinformatics and sequence analysis. These alignments may contain invaluable information that scientists need to predict the sequences' structures, determine the evolutionary relationships between them, or discover drug-like compounds that can bind to the sequences. Unfortunately, multiple sequence alignment (MSA) is NP-Complete. In addition, the lack of a reliable scoring method makes it very hard to align the sequences reliably and to evaluate the alignment outcomes. In this disser

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24

Garriga, Nogales Edgar 1990. "New algorithmic contributions for large scale multiple sequence alignments of protein sequences." Doctoral thesis, TDX (Tesis Doctorals en Xarxa), 2022. http://hdl.handle.net/10803/673526.

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In these days of significant changes and the rapid evolution of technology, the amount of datascience has to deal with the growth incredibly fast, and the size of data could be prohibitive.Multiple Sequence Alignments (MSA) are used in various areas of biology, and the increase ofdata has produced a degradation of the methods. That is why is proposed a new solution toperform the MSA. This novel paradigm allows the alignment of millions of sequences and theability to modularize the process. Regressive enables the parallelization of the process and thecombination of clustering methods (guide-tre

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25

Lu, Yue. "Improving the quality of multiple sequence alignment." [College Station, Tex. : Texas A&M University, 2008. http://hdl.handle.net/1969.1/ETD-TAMU-3111.

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26

Orobitg, Cortada Miquel. "High performance computing on biological sequence alignment." Doctoral thesis, Universitat de Lleida, 2013. http://hdl.handle.net/10803/110930.

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L'Alineament Múltiple de Seqüències (MSA) és una eina molt potent per a aplicacions biològiques importants. Els MSA són computacionalment complexos de calcular, i la majoria de les formulacions porten a problemes d'optimització NP-Hard. Per a dur a terme alineaments de milers de seqüències, nous desafiaments necessiten ser resolts per adaptar els algoritmes a l'era de la computació d'altes prestacions. En aquesta tesi es proposen tres aportacions diferents per resoldre algunes limitacions dels mètodes MSA. La primera proposta consisteix en un algoritme de construcció d'arbres guia per mill

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27

Yang, Qian 1973. "RNA sequence alignment and secondary structure prediction." Thesis, McGill University, 2005. http://digitool.Library.McGill.CA:80/R/?func=dbin-jump-full&object_id=82453.

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Functional RNA sequences typically have structural elements that are highly conserved during evolution. Here we present an algorithmic method for multiple alignment of RNAs, taking into consideration both structural similarity and sequence identity. Furthermore, we performed a comparative analysis on pairing probability matrices of a set of aligned orthologous sequences and predicted the conserved secondary structure. Our alignment method outperforms the most widely used multiple alignment tool - Clustal W, and the structure prediction approach we proposed can generate a more accurate s

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28

Holmes, I. "Studies in probabilistic sequence alignment and evolution." Thesis, University of Cambridge, 1999. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.604192.

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The complete sequencing of whole genomes presents opportunities for detailed study of molecular evolution. This thesis combines theoretical developments of Bayesian approaches in bioinformatics with analysis of duplications in the recently completed <I>C. elegans</I> genome. Developments in the Bayesian probabilistic framework for sequence analysis using hidden Markov models (HMMs) are described. The principal HMM algorithms are reviewed including alignment, training and model comparison. Theory is developed for prediction of alignment accuracy and tested using simulations. Software to provide

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29

Bulancea, Lindvall Oscar. "Quantum Methods for Sequence Alignment and Metagenomics." Thesis, KTH, Tillämpad fysik, 2019. http://urn.kb.se/resolve?urn=urn:nbn:se:kth:diva-256349.

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30

Büschking, Christian. "Incorporation of structural information in RNA sequence alignment." [S.l. : s.n.], 2001. http://deposit.ddb.de/cgi-bin/dokserv?idn=969343140.

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31

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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32

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

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33

Marco-Sola, Santiago. "Efficient approximate string matching techniques for sequence alignment." Doctoral thesis, Universitat Politècnica de Catalunya, 2017. http://hdl.handle.net/10803/460835.

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One of the outstanding milestones achieved in recent years in the field of biotechnology research has been the development of high-throughput sequencing (HTS). Due to the fact that at the moment it is technically impossible to decode the genome as a whole, HTS technologies read billions of relatively short chunks of a genome at random locations. Such reads then need to be located within a reference for the species being studied (that is aligned or mapped to the genome): for each read one identifies in the reference regions that share a large sequence similarity with it, therefore indicating wh

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34

Lightner, Carin Ann. "A Tabu Search Approach to Multiple Sequence Alignment." NCSU, 2008. http://www.lib.ncsu.edu/theses/available/etd-05312008-191232/.

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Sequence alignment methods are used to detect and quantify similarities between different DNA and protein sequences that may have evolved from a common ancestor. Effective sequence alignment methodologies also provide insight into the structure function of a sequence and are the first step in constructing evolutionary trees. In this dissertation, we use a tabu search approach to multiple sequence alignment. A tabu search is a heuristic approach that uses adaptive memory features to align multiple sequences. The adaptive memory feature, a tabu list, helps the search process avoid local optimal

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35

Talbot, Danielle. "Identifying misalignments in sequence alignment for protein modelling." Thesis, University of Reading, 2005. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.445754.

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36

Zhang, Xiaodong. "A Local Improvement Algorithm for Multiple Sequence Alignment." Ohio University / OhioLINK, 2003. http://rave.ohiolink.edu/etdc/view?acc_num=ohiou1049485762.

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37

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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38

Blassel, Luc. "From sequences to knowledge, improving and learning from sequence alignments." Electronic Thesis or Diss., Sorbonne université, 2022. http://www.theses.fr/2022SORUS385.

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Dans cette thèse nous étudierons deux problèmes importants en bioinformatique, le premier concernant l’analyse primaire de données de séquençage, et le second concernant l’analyse secondaire de séquence par apprentissage automatique en vue d’obtenir des connaissances biologiques. L’alignement de séquences est l’un des outils les plus puissants et les plus importants dans le domaine de la biologie computationnelle. L’alignement de lectures de séquençage est souvent la première étape de nombreuses analyses telles que la détection de variations de structure, ou l’assemblage de génomes. Les techno

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39

Li, Yuheng. "Searching for remotely homologous sequences in protein databases with hybrid PSI-blast." The Ohio State University, 2006. http://rave.ohiolink.edu/etdc/view?acc_num=osu1164741421.

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40

Ye, Yongtao, and 叶永滔. "Aligning multiple sequences adaptively." Thesis, The University of Hong Kong (Pokfulam, Hong Kong), 2014. http://hdl.handle.net/10722/206465.

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With the rapid development of genome sequencing, an ever-increasing number of molecular biology analyses rely on the construction of an accurate multiple sequence alignment (MSA), such as motifs detection, phylogeny inference and structure prediction. Although many methods have been developed during the last two decades, most of them may perform poorly on some types of inputs, in particular when families of sequences fall below thirty percent similarity. Therefore, this thesis introduced two different effective approaches to improve the overall quality of multiple sequence alignment. First,

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41

Nakato, Ryuichiro. "Development of Fast and Accurate Genomic Sequence Alignment Methods." 京都大学 (Kyoto University), 2010. http://hdl.handle.net/2433/123352.

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42

Zhang, Ching. "Genetic algorithm approaches for efficient multiple molecular sequence alignment." Thesis, National Library of Canada = Bibliothèque nationale du Canada, 1998. http://www.collectionscanada.ca/obj/s4/f2/dsk2/tape17/PQDD_0013/NQ30660.pdf.

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43

Zhou, Rong. "Memory-efficient graph search applied to multiple sequence alignment." Diss., Mississippi State : Mississippi State University, 2005. http://library.msstate.edu/etd/show.asp?etd=etd-06282005-015428.

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44

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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45

McMahon, Peter Leonard. "Accelerating genomic sequence alignment using high performance reconfigurable computers." Master's thesis, University of Cape Town, 2008. http://hdl.handle.net/11427/17377.

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Includes bibliographical references (pages 65-70).<br>Reconfigurable computing technology has progressed to a stage where it is now possible to achieve orders of magnitude performance and power efficiency gains over conventional computer architectures for a subset of high performance computing applications. In this thesis, we investigate the potential of reconfigurable computers to accelerate genomic sequence alignment specifically for genome sequencing applications. We present a highly optimized implementation of a parallel sequence alignment algorithm for the Berkeley Emulation Engine (BEE2)

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46

Jiang, Yanan master of cellular and molecular biology. "Manual alignment of IVS sequences and its implication in multiple sequence alignment." Thesis, 2011. http://hdl.handle.net/2152/ETD-UT-2011-12-4706.

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It is recognized that an iterative comparative analysis of large-scale homologous RNAs significantly promote the understanding of an RNA family. The Gutell lab is renowned for maintaining high quality RNA sequence alignments and accurately predicted RNA secondary structures using this approach. While the current available alignment and structure data are mainly obtained by trained domain experts with extensive manual effort, it is highly desired that this process is automated and replicable given the exponentially growing number of RNA sequence data and the amount of time required for expert t

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47

Ying, Chung Li, and 鍾立穎. "Multiple Sequence Alignment using Pairwise Suboptimal Alignment." Thesis, 2005. http://ndltd.ncl.edu.tw/handle/78872248303598965142.

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碩士<br>國立臺灣科技大學<br>資訊工程系<br>94<br>Multiple sequence alignment is an important tool to analysis biological sequence from searching similar sequence in database to protein structure. The optimal solution of dynamic programming is not always real biological solution when the number of sequence is increasing. Another method is progressive algorithm, it combined most similar sequence and then added next similar sequence. But the order of combining sequence have different alignment. Due to the optimal alignment is not always the best alignment in biological alignment, combining the pairwise suboptim

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Wang, Shu 1973. "On multiple sequence alignment." Thesis, 2007. http://hdl.handle.net/2152/3715.

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The tremendous increase in biological sequence data presents us with an opportunity to understand the molecular and cellular basis for cellular life. Comparative studies of these sequences have the potential, when applied with sufficient rigor, to decipher the structure, function, and evolution of cellular components. The accuracy and detail of these studies are directly proportional to the quality of these sequences alignments. Given the large number of sequences per family of interest, and the increasing number of families to study, improving the speed, accuracy and scalability of MSA is b

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Tsai, Ping Han, and 蔡秉翰. "Sequence Alignment with Block Constraint." Thesis, 2016. http://ndltd.ncl.edu.tw/handle/82895843637763555950.

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碩士<br>國立清華大學<br>資訊系統與應用研究所<br>104<br>In order to determine whether two sequences are similar or not, we usually do the pairwise alignment. In bioinformatics, sequence alignment is an important strategy to determine the identity between two DNA, RNA, or protein sequences. The sequence alignment can identify the similar regions that may share similar structure, function or evolutionary relationship. Compared with the 20-letter protein alphabet, the 4-letter RNA alphabet is smaller and less informative. As a consequence, when the identity between two RNA sequences is under 60%, it is hard to dete

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Xiao, Bo Weng, and èåæ. "Block Alignment: An Approach for Multiple Sequence Alignment Containing Clusters." Thesis, 2004. http://ndltd.ncl.edu.tw/handle/19616460760964410139.

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碩士<br>國立暨南國際大學<br>資訊工程學系<br>92<br>Multiple sequence alignment is a fundamental problem in computational molecular biology. It has been known as an NP-hard problem. To find its optimal solution will take a lot of time. For a reasonable wait and an acceptable solution, we have progressive methods. These methods perform pairwise alignment, and then combine them in to a multiple sequence alignment. In this thesis, we focus on multiple sequence alignment containing clusters. We try to take another view point to deal with sequence alignment. We use a matrix to present a sequence.

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