Dissertations / Theses on the topic 'Sequences'
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Cai, Zheng. "Repetitive sequence analysis for soybean genome sequences." Diss., Columbia, Mo. : University of Missouri-Columbia, 2005. http://hdl.handle.net/10355/4249.
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Thesis (M.S.)--University of Missouri-Columbia, 2005."May 2005" The entire dissertation/thesis text is included in the research.pdf file; the official abstract appears in the short.pdf file (which also appears in the research.pdf); a non-technical general description, or public abstract, appears in the public.pdf file. Includes bibliographical references.
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Parsons, Jeremy David. "Computer analysis of molecular sequences." Thesis, University of Cambridge, 1993. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.282922.
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Kimothi, Dhananjay. "Learning representations for molecular sequences." Thesis, Queensland University of Technology, 2021. https://eprints.qut.edu.au/226106/1/Dhananjay_Kimothi_Thesis.pdf.
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This thesis explores the utility of representation learning for bioinformatics applications. It proposes approaches for generating low dimensional embeddings for molecular sequences, which proved effective for downstream bioinformatics tasks such as protein classification and protein-protein interaction prediction. One specific theme of this thesis is to develop a scalable and computationally effective solution for large scale sequence comparisons and two successful approaches – one based on a hierarchy of models, the other on a hybrid of two methods – are presented. The representation learning approaches proposed in this thesis are generic and can be adapted for similar problems within bioinformatics and other domains.
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VITTE, PATRICK. "Plus longue sous-sequence commune et analyse de sequences biologiques." Aix-Marseille 2, 1996. http://www.theses.fr/1996AIX22073.
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Cette these est consacree a l'etude des plus longues sous-sequences communes (lcs) a un ensemble de chaines de caracteres et a leur usage dans l'analyse des sequences biologiques. En deux mots, une sous-sequence commune a plusieurs chaines est une suite de caracteres, pas necessairement consecutifs, que l'on trouve dans le meme ordre dans chaque chaine. Les lcs nous interesse selon deux points de vue: algorithmique: peut-on determiner, approximer et encadrer leur longueur ? comment construire une lcs ? peut-on les enumerer ? ces questions sont classiques en optimisation combinatoire et nous avons developpe une methode de construction d'une lcs. Le probleme etant np-difficile, nous avons defini une methode approchee, de complexite polynomiale, dont nous avons etudie les performances. Biologique: nous montrons certaines applications des lcs dans l'analyse des sequences biologiques. D'abord en definissant une distance qui permet de retrouver des sequences voisines et de classer un nouvel element dans un arbre de sequences. Puis en proposant une methode d'alignement multiple d'une famille de sequences proteiques
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Pray, Keith A. "Apriori Sets And Sequences: Mining Association Rules from Time Sequence Attributes." Link to electronic thesis, 2004. http://www.wpi.edu/Pubs/ETD/Available/etd-0506104-150831/.
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Thesis (M.S.) -- Worcester Polytechnic Institute.Keywords: mining complex data; temporal association rules; computer system performance; stock market analysis; sleep disorder data. Includes bibliographical references (p. 79-85).
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Faulkner, Sean (Sean Anthony) Carleton University Dissertation Engineering Electrical. "Composite sequences for rapid acquisition of direct-sequence spread spectrum signals." Ottawa, 1992.
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Seth, Pawan. "STUDY OF THE RELATIONSHIP BETWEEN Mus musculus PROTEIN SEQUENCES AND THEIR BIOLOGICAL FUNCTIONS." University of Akron / OhioLINK, 2007. http://rave.ohiolink.edu/etdc/view?acc_num=akron1176736255.
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Lui, Man-Cheung Max. "Generation and evaluation of mechanical assembly sequences using the liaison-sequence method." Thesis, Massachusetts Institute of Technology, 1988. http://hdl.handle.net/1721.1/14544.
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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-tree) with whatever aligner is desired. On theclustering side, the guide-tree has to be rethought. A study of the current state of the methodsand their strength and weaknesses have been performed to shed some light on the topic. Theguide-tree cannot be the bottleneck, and it should provide a good starting point for the aligners.En aquests dies de profunds canvis i una ràpida evolució de la tecnologia, la quantitat de dataque la ciència ha de treballar ha crescut increïblement ràpid i la grandària dels arxius ha crescutde manera quasi prohibitiva.Els alineaments múltiples de seqüència (MSA) es fan servir endiverses àrees de la biologia, i l'increment de les dades ha produït una degradació delsresultats. És per això, que es proposa una nova estratègia per realitzar els alineaments. Aquestnou paradigma permet alinear milions de seqüències i l'opcio de modularitzar el procés.'Regressive' permet la paral·lelització del procés i la combinació de diferents algoritmesd'agrupacio (guide-tree) amb el mètode de alineament que és desitgi. Dins del camp del'agrupació, s'ha de repensar l'estratègia per crear els guide-tree. Un estudi sobre l'estat actualdels mètodes i les seves virtuts i punts febles ha sigut realitzar per llençar una mica de llum enaquesta àrea. Els 'guide-tree' no poden ser el coll de botella, i haurien de servir per començarde la millor manera possible el procés d'alineament.
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Winebarger, Onnie Lynn. "k-Interpolated sequences." [Bloomington, Ind.] : Indiana University, 2006. http://gateway.proquest.com/openurl?url_ver=Z39.88-2004&rft_val_fmt=info:ofi/fmt:kev:mtx:dissertation&res_dat=xri:pqdiss&rft_dat=xri:pqdiss:3229597.
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Thesis (Ph.D.)--Indiana University, Dept. of Mathematics, 2006."Title from dissertation home page (viewed July 11, 2007)." Source: Dissertation Abstracts International, Volume: 67-08, Section: B, page: 4466. Adviser: Daniel P. Maki.
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Astrovskaya, Irina A. "Inferring Genomic Sequences." Digital Archive @ GSU, 2011. http://digitalarchive.gsu.edu/cs_diss/59.
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Recent advances in next generation sequencing have provided unprecedented opportunities for high-throughput genomic research, inexpensively producing millions of genomic sequences in a single run. Analysis of massive volumes of data results in a more accurate picture of the genome complexity and requires adequate bioinformatics support. We explore computational challenges of applying next generation sequencing to particular applications, focusing on the problem of reconstructing viral quasispecies spectrum from pyrosequencing shotgun reads and problem of inferring informative single nucleotide polymorphisms (SNPs), statistically covering genetic variation of a genome region in genome-wide association studies.
The genomic diversity of viral quasispecies is a subject of a great interest, particularly for chronic infections, since it can lead to resistance to existing therapies. High-throughput sequencing is a promising approach to characterizing viral diversity, but unfortunately standard assembly software cannot be used to simultaneously assemble and estimate the abundance of multiple closely related (but non-identical) quasispecies sequences. Here, we introduce a new Viral Spectrum Assembler (ViSpA) for inferring quasispecies spectrum and compare it with the state-of-the-art ShoRAH tool on both synthetic and real 454 pyrosequencing shotgun reads from HCV and HIV quasispecies. While ShoRAH has an advanced error correction algorithm, ViSpA is better at quasispecies assembling, producing more accurate reconstruction of a viral population. We also foresee ViSpA application to the analysis of high-throughput sequencing data from bacterial metagenomic samples and ecological samples of eukaryote populations.
Due to the large data volume in genome-wide association studies, it is desirable to find a small subset of SNPs (tags) that covers the genetic variation of the entire set. We explore the trade-off between the number of tags used per non-tagged SNP and possible overfitting and propose an efficient 2LR-Tagging heuristic.
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Freed, Denise E., Ulrich M. Scheven, and Martin D. Hürlimann. "Split 180° sequences." Universitätsbibliothek Leipzig, 2015. http://nbn-resolving.de/urn:nbn:de:bsz:15-qucosa-192244.
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In applications of NMR in inhomogeneous fields, sequences based on the Carr-Purcell-Meiboom-Gill (CPMG) sequence play a central role. The standard CPMG sequence consists of an initial 90° excitation pulse, followed by a long string of 180° refocusing pulses. This creates a series of echoes that decay with characteristic relaxation time T2eff. Here we present a modified sequence, the Split-180° sequence that specifically takes advantage of grossly inhomogeneous fields. In its simplest implementation, the 180° refocusing
pulse of the CPMG sequence is split into two separate pulses. This sequence, which can be viewed as a modification of the CPMG sequence, simultaneously generates two types of signal that can be separately detected. One is a CPMG-like signal that decays with the expected relaxation time T2eff. In addition, a second type of signal builds up and approaches a steady-state. The amplitude of this dynamic equilibrium depends on the ratio of the longitudinal to the transverse relaxation times, T1/T2. We present experimental results and summarize the new theory that describes both signals in a unified manner.
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Freed, Denise E., Ulrich M. Scheven, and Martin D. Hürlimann. "Split 180° sequences." Diffusion fundamentals 10 (2009) 19, S. 1-3, 2009. https://ul.qucosa.de/id/qucosa%3A14110.
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In applications of NMR in inhomogeneous fields, sequences based on the Carr-Purcell-Meiboom-Gill (CPMG) sequence play a central role. The standard CPMG sequence consists of an initial 90° excitation pulse, followed by a long string of 180° refocusing pulses. This creates a series of echoes that decay with characteristic relaxation time T2eff. Here we present a modified sequence, the Split-180° sequence that specifically takes advantage of grossly inhomogeneous fields. In its simplest implementation, the 180° refocusing
pulse of the CPMG sequence is split into two separate pulses. This sequence, which can be viewed as a modification of the CPMG sequence, simultaneously generates two types of signal that can be separately detected. One is a CPMG-like signal that decays with the expected relaxation time T2eff. In addition, a second type of signal builds up and approaches a steady-state. The amplitude of this dynamic equilibrium depends on the ratio of the longitudinal to the transverse relaxation times, T1/T2. We present experimental results and summarize the new theory that describes both signals in a unified manner.
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Shipsey, Rachel Elizabeth. "Elliptic divisibility sequences." Thesis, Goldsmiths College (University of London), 2000. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.392661.
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Lomas, Martin John. "A bioinformatics analysis of sequences and sequence libraries from the moss Physcomitrella patens." Thesis, University of Leeds, 2003. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.396944.
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Farrington, Paul. "The behaviour of sequence transformations as applied to slowly converging sequences and series." Thesis, Keele University, 2001. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.327636.
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Ritter, Geoffrey William. "Lithofaces and Sequence Architecture of the Upper Paradox Formation (Middle Pennsylvanian)in the Subsurface Northern Blanding Subbasin, Paradox Basin, Utah." BYU ScholarsArchive, 2018. https://scholarsarchive.byu.edu/etd/7319.
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THE PARADOX Basin is a northwest-southeast trending intracratonic basin that formedin southwestern Colorado, southeastern Utah and adjacent parts of Arizona and New Mexicoduring the late Paleozoic Era. During rise of the adjacent Uncompahgre Uplift (Ancestral RockyMountains) the rapidly subsiding basin was filled with over 2000 m of Permo-Pennsylvaniansediments. Stacked depositional sequences accumulated in three roughly parallel facies belts: anortheastern clastic belt (adjacent to uplift), a central salt and black shale belt, and asouthwestern carbonate belt. Over 400 million barrels of oil have been extracted from upperParadox (Desert Creek and Ismay) carbonates in the southern Blanding Subbasin (Greater AnethField) since 1956. The sedimentology and sequence stratigraphy of Paradox Shelf strata on thewalls of the San Juan River gorge and in the subsurface Aneth Buildup are well documented.Less well documented are the stratigraphy and facies architecture of basinward extensions ofupper Paradox sequences in the northern part of the Blanding Subbasin.Detailed analysis of the lower and upper Desert Creek and lower and upper Ismay 4thordersequences from three cores (Long Point, Lewis Road, Cedar Point) demonstrate theexistence of distinctive basinward depositional trends. Compared to sequences exposed on theParadox Shelf (San Juan River outcrops) and the Aneth Buildup, sequences in the more distalnorthern Blanding Subbasin are thinner, are dominated by muddy carbonate facies, displaylimited occurrences of porous phylloid-algal and oolitic carbonates, contain thicker, morecomplete occurrences of black shale, and possess distinctive suites of lowstand facies (quartzsandstone on the shelf, bedded and nodular evaporates in the basin). Vertically, the four 4th-ordersequences display 2nd-order progradation of the Paradox Shelf through Desert Creek and Ismaytime. Carbonate-starved sequences (4th order) and parasequences (5th order) comprised of muddominatedfacies are succeeded upward by thicker, more grain-rich sequences andparasequences. The implications for the petroleum system relative to established oil and gasfields is that conventional reservoir rock facies are rare, except in small, isolated buildups.Meteoric diagenesis associated with 4th-order lowstands of sea level has reduced overallpermeability. Lowstand conditions also promoted limited precipitation of pore-occludingevaporite cement. The maximum-flood Chimney Rock, Gothic and Hovenweep shales arethicker and contain a more complete succession of basinal cycles than updip occurrences of thesepetroleum source rocks. A suite of samples from the Gothic Shale from the Cedar Point coreindicate higher burial maturity (kerogen has mostly been converted to gas) compared to valuesderived from the outcrop belt and more proximal subsurface samples.
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Lampard, Gregory Raymond. "Expression of foreign gene sequences mediated by chicken lysozyme gene regulatory sequences." Thesis, National Library of Canada = Bibliothèque nationale du Canada, 2001. http://www.collectionscanada.ca/obj/s4/f2/dsk3/ftp04/MQ61918.pdf.
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Surovy, Martin. "Matrix Kundt-Newman sequences." Thesis, National Library of Canada = Bibliothèque nationale du Canada, 1998. http://www.collectionscanada.ca/obj/s4/f2/dsk2/tape15/PQDD_0013/MQ35001.pdf.
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McLeod, Alice 1977. "Counts of binary sequences." Thesis, McGill University, 2002. http://digitool.Library.McGill.CA:80/R/?func=dbin-jump-full&object_id=29457.
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Many classes of linear and cyclic binary strings are counted using a particularly elementary counting technique. Most of these enumerations are much simpler and more elementary than those found in the literature. Applications of these counts to other combinatorial problems are described. An apparently new identity for Lucas numbers is established; it shows how to express an arbitrary product of Lucas numbers as a sum of Lucas numbers.
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Lothian, Paul James Gillougley. "On correlations of sequences." Thesis, Royal Holloway, University of London, 1998. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.286326.
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丁嘉慧 and Ka-wai Ting. "Time sequences: data mining." Thesis, The University of Hong Kong (Pokfulam, Hong Kong), 2001. http://hub.hku.hk/bib/B31226760.
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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, by considering the similarity of the input sequences, we proposed an adaptive approach to compute better substitution matrices for each pair of sequences, and then apply the progressive alignment method to align them. For example, for inputs with high similarity, we consider the whole sequences and align them with global pair-Hidden Markov model, while for those with moderate low similarity, we may ignore the ank regions and use some local pair-Hidden Markov models to align them. To test the effectiveness of this approach, we have implemented a multiple sequence alignment tool called GLProbs and compared its performance with one dozen leading tools on three benchmark alignment databases, and GLProbs' alignments have the best scores in almost all testings. We have also evaluated the practicability of the alignments of GLProbs by applying the tool to three biological applications, namely phylogenetic tree reconstruction, protein secondary structure prediction and the detection of high risk members for cervical cancer in the HPV-E6 family, and the results are very encouraging.
Second, based on our previous study, we proposed another new tool PnpProbs, which constructs better multiple sequence alignments by better handling of guide trees. It classifies input sequences into two types: normally related sequences and distantly related sequences. For normally related sequences, it uses an adaptive approach to construct the guide tree, and based on this guide tree, aligns the sequences progressively. To be more precise, it first estimates the input's discrepancy by computing the standard deviation of their percent identities, and based on this estimate, it chooses the best method to construct the guide tree. For distantly related sequences, PnpProbs abandons the guide tree; instead it uses the non-progressive sequence annealing method to construct the multiple sequence alignment. By combining the strength of the progressive and non-progressive methods, and with a better way to construct the guide tree, PnpProbs improves the quality of multiple sequence alignments significantly for not only general input sequences, but also those very distantly related.
With those encouraging empirical results, our developed software tools have been appreciated by the community gradually. For example, GLProbs has been invited and incorporated into the JAva Bioinformatics Analysis Web Services system (JABAWS).published_or_final_version
Computer Science
Master
Master of Philosophy
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Lauder, Alan George Beattie. "Continued fractions and sequences." Thesis, Royal Holloway, University of London, 1999. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.325109.
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ABDEDDAIM, SAID. "Comparaison de sequences biologiques." Paris 6, 1996. http://www.theses.fr/1996PA066449.
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Cette these porte sur l'alignement de sequences, et plus particulierement sur l'alignement de plus de deux sequences biologiques. Les algorithmes que nous avons developpes operent en deux etapes : dans une premiere etape des blocs (alignements d'occurences de facteurs) compatibles sont selectionnes dans les sequences, la seconde etape consiste a aligner les sequences entre les blocs. Notre strategie de selection des blocs, est une strategie gloutonne tout en etant prudente. Nous nous interessons particulierement au calculde blocs qui ne concernent pas necessairement toutes les sequences a aligner. Pour calculer efficacement ces blocs, nous definissons la structure de graphe hybride, dans lequel un chemin reliant deux occurences signifie que celles-ci ne peuvent faire partie d'un bloc compatible avec les blocs precedemment selectionnes. La prise en compte d'un nouveau bloc se traduit par l'insertion d'aretes dans le graphe hybride. Nous decrirons un nouvel algorithme incremental permettant de maintenir la fermeture transive de la relation decrite par le graphe hybride apres l'insertion d'un bloc. Sous certaines hypotheses, induites par l'observation d'alignement fait a la main, nous montrons que l'on peut efficacement aligner les sequences entre les blocs a l'aide d'un algorithme de programmation dynamique que nous avons developpe. Nous illustrons sur des donnees reelles l'efficacite (en temps de calcul et qualite des alignements) de nos algorithmes compares a deux programmes usites clustal w et treealing.
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Aebischer, Beat. "Sequences of Möbius transformations /." Bern, 1989. http://www.ub.unibe.ch/content/bibliotheken_sammlungen/sondersammlungen/dissen_bestellformular/index_ger.html.
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陳子健 and Chi-kin John Baptist Chan. "A study of binary sequences for direct-sequence spread-spectrum multiple-access communication systems." Thesis, The University of Hong Kong (Pokfulam, Hong Kong), 1996. http://hub.hku.hk/bib/B31212761.
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Chan, Chi-kin John Baptist. "A study of binary sequences for direct-sequence spread-spectrum multiple-access communication systems /." Hong Kong : University of Hong Kong, 1996. http://sunzi.lib.hku.hk/hkuto/record.jsp?B16043005.
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Johnson, Penelope A. "Isolation and characterization of Drosophila melanogaster genomic DNA sequences containing bacterial insertion sequences." Thesis, University of Ottawa (Canada), 1987. http://hdl.handle.net/10393/5227.
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Arner, Erik. "Solving repeat problems in shotgun sequencing /." Stockholm, 2006. http://diss.kib.ki.se/2006/91-7140-996-3/.
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Aniba, Mohamed Radhouane. "Knowledge based expert system development in bioinformatics : applied to multiple sequence alignment of protein sequences." Strasbourg, 2010. https://publication-theses.unistra.fr/public/theses_doctorat/2010/ANIBA_Mohamed_Radhouane_2010.pdf.
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L'objectif de ce projet de thèse a été le développement d'un système expert afin de tester, évaluer et d'optimiser toutes les étapes de la construction et l'analyse d'un alignement multiple de séquences. Le nouveau système a été validé en utilisant des alignements de référence et apporte une nouvelle vision pour le développement de logiciels en bioinformatique: les systèmes experts basés sur la connaissance. L'architecture utilisée pour construire le système expert est très modulaire et flexible, permettant à AlexSys d'évoluer en même temps que de nouveaux algorithmes seront mis à disposition. Ultérieurement, AlexSys sera utilisé pour optimiser davantage chaque étape du processus d'alignement, par exemple en optimisant les paramètres des différents programmes d 'alignement. Le moteur d'inférence pourrait également être étendu à identification des combinaisons d'algorithmes qui pourraient fournir des informations complémentaires sur les séquences. Par exemple, les régions bien alignées par différents algorithmes pourraient être identifiées et regroupées en un alignement consensus unique. Des informations structurales et fonctionnelles supplémentaires peuvent également être utilisées pour améliorer la précision de l'alignement final. Enfin, un aspect crucial de tout outil bioinformatique consiste en son accessibilité et la convivialité d' utilisation. Par conséquent, nous sommes en train de développer un serveur web, et un service web, nous allons également concevoir un nouveau module de visualisation qui fournira une interface intuitive et conviviale pour toutes les informa ions récupérées et construites par AlexSysThe objective of this PhD project was the development of an integrated expert system to test, evaluate and optimize all the stages of the construction and the analysis of a multiple sequence alignment. The new system was validated using standard benchmark cases and brings a ncw vision to software development in Bioinformatics: knowledge-guided systems. The architecture used to build the expert system is highly modular and flcxible, allowing AlcxSys to evolve as new algorithms are made available. In the future, AlexSys will he uscd to furthcr optimize each stage of the alignment process, for example by optimizing the input parameters of the different algorithms. The inference engine could also be extended to identify combinations of algorithms that could potentially provide complementary information about the input sequences. For example, well aligned regions from different aligners could be identified and combined into a single consensus alignment. Additional structural and functional information could also be exploited to improve the final alignment accuracy. Finally, a crucial aspect of any bioinformatics tool is its accessibility and usability. Therefore, we are currently developing a web server, and a web services based distributed system. We will also design a novel visualization module that will provide an intuitive, user-friendly interface to all the information retrieved and constructed by AlexSys
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Risley, Rebecca N. "A Generalization of Sturmian Sequences: Combinatorial Structure and Transcendence." Thesis, University of North Texas, 1998. https://digital.library.unt.edu/ark:/67531/metadc278440/.
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We investigate a class of minimal sequences on a finite alphabet Ak = {1,2,...,k} having (k - 1)n + 1 distinct subwords of length n. These sequences, originally defined by P. Arnoux and G. Rauzy, are a natural generalization of binary Sturmian sequences. We describe two simple combinatorial algorithms for constructing characteristic Arnoux-Rauzy sequences (one of which is new even in the Sturmian case). Arnoux-Rauzy sequences arising from fixed points of primitive morphisms are characterized by an underlying periodic structure. We show that every Arnoux-Rauzy sequence contains arbitrarily large subwords of the form V^2+ε and, in the Sturmian case, arbitrarily large subwords of the form V^3+ε. Finally, we prove that an irrational number whose base b-digit expansion is an Arnoux-Rauzy sequence is transcendental.
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Blanco, García Enrique. "Meta-alignment of biological sequences." Doctoral thesis, Universitat Politècnica de Catalunya, 2006. http://hdl.handle.net/10803/6654.
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Les seqüències són una de les estructures de dades més versàtils que existeixen. De forma relativament senzilla, en una seqüència de símbols es pot emmagatzemar informació de qualsevol tipus. L'anàlisi sistemàtic de seqüències es un àrea molt rica de l'algorísmica amb numeroses aproximacions desenvolupades amb éxit. En concret, la comparació de seqüències mitjançant l'alineament d'aquestes és una de les eines més potents. Una de les aproximacions més populars i eficients per alinear dues seqüències es l'ús de la programació dinàmica. Malgrat la seva evident utilitat, un alineament de dues seqüències no és sempre la millor opció per a caracteritzar la seva funció. Moltes vegades, les seqüències codifiquen la informació en diferents nivells (meta-informació). És llavors quan la comparació directa entre dues seqüències no es capaç de revelar aquelles estructures d'ordre superior que podrien explicar la relació establerta entre aquestes seqüències.
Amb aquest treball hem contribuït a millorar la forma en que dues seqüències poden ser comparades, desenvolupant una família d'algorismes d'alineament de la informació d'alt nivell codificada en seqüències biològiques (meta-alineaments). Inicialment, hem redissenyat un antic algorisme, basat en programació dinàmica, que és capaç d'alinear dues seqüències de meta-informació, procedint després a introduir-hi vàries millores per accelerar la seva velocitat. A continuació hem desenvolupat un algorisme de meta-aliniament capaç d'alinear un número múltiple de seqüències, combinant l'algorisme general amb un esquema de clustering jeràrquic. A més, hem estudiat les propietats dels meta-alineaments produïts, modificant l'algorisme per tal d'identificar alineaments amb una configuració no necessàriament col.lineal, el que permet llavors la detecció de permutacions en els resultats.
La vida molecular és un exemple paradigmátic de la versatilitat de les seqüències. Les comparaciones entre genomes, ara que la seva seqüència està disponible, permeten identificar numerosos elements biològicament funcionals. La seqüència de nucleòtids de molts gens, per exemple, es troba acceptablement conservada entre diferents espècies. En canvi, les seqüències que regulen la activació dels propis gens són més curtes i variables. Així l'activació simultànea d'un conjunt de gens es pot explicar només a partir de la conservació de configuracions comunes d'elements reguladors d'alt nivell i no pas a partir de la simple conservació de les seves seqüències. Per tant, hem entrenat els nostres programes de meta-alineament en una sèrie de conjunts de regions reguladores recopilades per nosaltres mateixos de la literatura i desprès, hem provat la utilitat biològica de la nostra aproximació, caracteritzant automàticament de forma exitosa les regions activadores de gens humans conservats en altres espècies.
The sequences are very versatile data structures. In a straightforward manner, a sequence of symbols can store any type of information. Systematic analysis of sequences is a very rich area of algorithmics, with lots of successful applications. The comparison by sequence alignment is a very powerful analysis tool. Dynamic programming is one of the most popular and efficient approaches to align two sequences. However, despite their utility, alignments are not always the best option for characterizing the function of two sequences. Sequences often encode information in different levels of organization (meta-information). In these cases, direct sequence comparison is not able to unveil those higher-order structures that can actually explain the relationship between the sequences.
We have contributed with the work presented here to improve the way in which two sequences can be compared, developing a new family of algorithms that align high level information encoded in biological sequences (meta-alignment). Initially, we have redesigned an existent algorithm, based in dynamic programming, to align two sequences of meta-information, introducing later several improvements for a better performance. Next, we have developed a multiple meta-alignment algorithm, by combining the general algorithm with the progressive schema. In addition, we have studied the properties of the resulting meta-alignments, modifying the algorithm to identify non-collinear or permuted configurations.
Molecular life is a great example of the sequence versatility. Comparative genomics provide the identification of numerous biologically functional elements. The nucleotide sequence of many genes, for example, is relatively well conserved between different species. In contrast, the sequences that regulate the gene expression are shorter and weaker. Thus, the simultaneous activation of a set of genes only can be explained in terms of conservation between configurations of higher-order regulatory elements, that can not be detected at the sequence level. We, therefore, have trained our meta-alignment programs in several datasets of regulatory regions collected from the literature. Then, we have tested the accuracy of our approximation to successfully characterize the promoter regions of human genes and their orthologs in other species.
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Llinàs, i. Grau Mireia. "Verbal Sequences: A Generative Approach." Doctoral thesis, Universitat Autònoma de Barcelona, 1990. http://hdl.handle.net/10803/4916.
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Aquesta tesi vol proporcionar una explicació a un constrast sintàctic entre l'anglès, el català i l'espanyol tot assumint propostes teòriques específiques del marc generativista dins del model de la Recció i el Lligam. Aquestes llengües construeixen les seves seqüències verbals amb auxiliars i verbs lèxics, com es veu als exemples següents:
(1) La Maria ha ballat a la festa
(2) María ha bailado en la fiesta
(3) Mary has danced at the party
No obstant, quan s'introdueixen altres elements a les oracions, el comportament de l'auxiliar i el verb lèxic contrasta entre l'anglès i les altres dues llengües:
(4) Ha ballat la María a la festa?
(5) Ha bailado María en la fiesta?
(6) Has Mary danced at the party?
(7) La María no ha ballat a la festa
(8) María no ha bailado en la fiesta
(9) Mary has not danced at the party
Com es pot observar, la seqüència AUX+V en català i espanyol ha de romandre adjacent en la construcció interrogativa i la negativa. En anglès, la seqüència s'ha de separar; l'auxiliar passa a ocupar la posició inicial a la interrogativa i la partícula negativa intervé entre l'auxiliar i el verb lèxic.
La tesi proporciona una descripció del comportament sintàctic de diverses constructions verbals. Inclou no tan sols les seqüències d'auxilliar i verb lèxic exemplificades més amunt sinó també altres seqüències conegudes com a predicats complexos ( que inclouen tant verbs causatius, com modals o aspectuals).
La tesi també analitza un altre constrast que trobem en la sintaxi de les dues llengües romàniques estudiades, es tracta de l'alt grau de cohesió entre els auxiliars i els verbs lèxics en contrast amb les combinacions de verbs causatius, modals o aspectuals i un verb lèxic. S'utilitzen diferents proves sintàcitques per comprovar el grau de cohesió de les seqüències, com ara la pujada del clític.
El segon capítol de la tesi inclou una revisió panoràmica de la literatura rellevant del tema. L'objectiu d'aquesta revisió és determinar el grau de cohesió entre els elements verbals de cada construcció, proposar una estructura sintàctica bàsica i descobrir el mecanisme responsable dels contrastos observats.
El capítol tercer explica aquest mecanisme, que és el que es pren com a base de les diferències de grau de cohesió observades entre els elements verbals analitzats. El mecanisme és el de la incorporació (Baker 1988), un moviment essencial de nucli-a-nucli altament actiu enllengües polisintètiques com ara el Chichewa.
La tesi inclou un capítol d'introducció al marc teòric (capítol 1) i un capítol final on s'exposen algunes consideracions de com adaptar les propostes estrcturals de la tesi a la teoria emergent de les categories funcionals (capítol 4).
Esta tesis quiere proporcionar una explicación a un contraste sintáctico entre el inglés, el catalán i el español asumiendo propuestas teóricas específicas del marco generativista dentro del modelo de la Rección y el Ligamiento.
Estas tres lenguas construyen sus secuencias verbales con un auxiliar y un verbo léxico, com vemos en los siguientes ejemplos:
(1) La Maria ha ballat a la festa
(2) María ha bailado en la fiesta
(3) Mary has danced at the party
No obstante, cuando se introducen otros elementos en las oraciones, el comportamiento del auxiliar y el verbo léxico contrasta entre el inglés y las otras dos lenguas:
(4) Ha ballat la María a la festa?
(5) Ha bailado María en la fiesta?
(6) Has Mary danced at the party?
(7) La María no ha ballat a la festa
(8) María no ha bailado en la fiesta
(9) Mary has not danced at the party
Como se puede observar, la secuencia AUX+V en catalán y español debe permanecer adyacente en la construcción interrogativa y en la negativa. En inglés, la secuencia se debe separar; el auxliar pasa a ocupar la posición inicial en la interrogativa y la partícula negativa interviene entre el auxiliar y el verbo léxico.
La tesis proporciona una descripción del comportamiento sintáctico de varias construcciones verbales. Incluye no tan solo las secuencias de auxiliar y verbo ejemplificadas aquí, sino también otras conocidas como predicados complejos (que incluyen verbos causaticos, modales y aspectuales).
La tesis también analiza otro contraste que encontramos en la sintaxis de las dos lenguas románicas estudiadas, se trata del alto grado de cohesión entre las secuencias de auxiliar y verbo léxico en contraste con las combinaciones de verbos causativos, modales y apectuales con un verbo léxico. Se utilizan varias pruebas sintácticas para comprobar el grado de cohesión entre los elemntos verbales como la subida de clítico.
El segundo capítulo de la tesis incluye una revisión panorámica de la literatura relevante sobre el tema. El objetivo de esta revisión es determinar el grado de cohesión entre los elementos verbales de cada construcción, proponer una estructura sintáctica básica, y descubrir el mecanismo responsable de los contrastes observados.
El tercer capítulo explica este mecanismo, que se toma como base de las diferencias en el grado de cohesión observadas entre los elementos verbales analizados. El mecanismo es el de la incorporación (Baker 1988) , un movimiento esencial de núcleo-a-núcleo altamente activo en las lenguas polisintéticas com el Chichewa.
La tesis incluye un capítulo de introducción al marco teórico (capítulo 1) y un capítulo final donde se hacen consideraciones sobre como adaptar las propuestas estructurales de la tesis a la teoría emergente de las categorías funcionales (capítulo 4).
This thesis attempts to provide an explanation of a syntactic contrast between English, Catalan and Spanish assuming specific theoretical proposals in the generative framework within the Government and Binding model.
These languages construct their verbal sequences by means of auxiliaries and lexical verbs, as in the following examples:
(1) La Maria ha ballat a la festa
(2) María ha bailado en la fiesta
(3) Mary has danced at the party
Nevertheless, when other elements are introduced in the sentences, the behaviour of the auxiliary and the lexical verb constrasts between English and the other two languages:
(4) Ha ballat la María a la festa?
(5) Ha bailado María en la fiesta?
(6) Has Mary danced at the party?
(7) La María no ha ballat a la festa
(8) María no ha bailado en la fiesta
(9) Mary has not danced at the party
As can be observed, the verbal sequence AUX+V in Catalan and Spanish must remain adjacent in the interrogative and the negative constructions. In English, the sequence must be separated, the auxiliary is placed in the initial position in the interrogative and the negative particle intervenes between the auxiliary and the lexical verb.
The thesis provides a description of the behaviour of several verbal constructions. It includes not only the verbal sequences of auxiliaries plus lexical verbs exemplified above but also other sequences known as complex predicates (including causative, aspectual and modal verbs).
The thesis also analyses another contrast found in the syntax of the two Romance languages studied, namely a higher degree of cohesion between auxiliaries and lexical verbs contrasting with the combination of a causative, aspectual or modal verb and a lexical verb. Several syntactic tests are used to assess the degree of cohesion, such as clitic-climbing.
The second chapter of the thesis includes an overview of the relevant literature on the subject. The focus of the overview is to determine the degree of cohesion between the verbal elements in each of the constructions, to propose a basic syntactic structure and to discover the mechanism responsible for the constrasts observed.
The third chapter of the thesis explains this mechanism which is taken to be responsible for the differences in degree of cohesion of the sequences analysed. The mechanism is known as incorporation (Baker 1988), an essential head-to-head movement which is highly active in polysynthetic languages like Chichewa.
The thesis includes a chapter of introduction to the framework (chapter 1) and a final chapter where some considerations are made on how to adapt the structural proposals in the thesis to the emerging theory of functional categories (chapter 4).
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Hertel, Doreen. "Crosscorrelation properties between perfect sequences." [S.l.] : [s.n.], 2007. http://deposit.ddb.de/cgi-bin/dokserv?idn=983650411.
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Palmacci, Matthew Stephen. "Escher's problem and numerical sequences." Link to electronic thesis, 2006. http://www.wpi.edu/Pubs/ETD/Available/etd-042706-133106/.
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Sandve, Geir Kjetil. "Motif discovery in biological sequences." Thesis, Norwegian University of Science and Technology, Department of Computer and Information Science, 2005. http://urn.kb.se/resolve?urn=urn:nbn:no:ntnu:diva-9270.
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This master thesis is a Ph.D. research plan for motif discovery in biological sequences, and consists of three main parts. Chapter 2 is a survey of methods for motif discovery in DNA regulatory regions, with a special emphasis on computational models. The survey presents an integrated model of the problem that allows systematic and coherent treatment of the surveyed methods. Chapter 3 presents a new algorithm for composite motif discovery in biological sequences. This algorithm has been used with success for motif discovery in protein sequences, and will in future work be extended on to explore properties of the DNA regulatory mechanism. Finally, chapter 4 describes several current research projects, as well as some more general future directions of research. The research focuses on the development of new algorithms for the discovery of composite motifs in DNA. These algorithms will partly be used for systematic exploration of the DNA regulatory mechanism. An increased understanding of this mechanism may lead to more accurate computational models, and hence more sensitive motif discovery methods.
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Shi, Yifan. "Representing and Recognizing Temporal Sequences." Diss., Georgia Institute of Technology, 2006. http://hdl.handle.net/1853/13992.
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Activity recognition falls in general area of pattern recognition, but it resides mainly in temporal domain which leads to distinctive characteristics. We provide an extensive survey over existing tools including FSM, HMM, BNT, DBN, SCFG and Symbolic Network Approach (PNF-network). These tools are inefficient to meet many of the requirements of activity recognition, leading to this work to develop a new graphical model: Propagation Net (P-Net).
Many activities can be represented by a partially ordered set of temporal intervals, each of which corresponds to a primitive motion. Each interval has both temporal and logical constraints that control the duration of the interval and its relationship with other intervals. P-Net takes advantage of such fundamental constraints that it provides an graphical conceptual model to describe the human knowledge and an efficient computational model to facilitate recognition and learning.
P-Nets define an exponentially large joint distribution that standard bayesian inference cannot handle. We devise two approximation algorithms to interpret a multi-dimensional observation sequence of evidence as a multi-stream propagation process through P-Net. First, Local Maximal Search Algorithm (LMSA) is constructed with polynomial complexity; Second, we introduce a particle filter based framework, Discrete Condensation (D-Condensation) algorithm, which samples the discrete state space more efficiently then original Condensation.
To construct a P-Net based system, we need two parts: P-Net and the corresponding detector set. Given topology information and detector library, P-Net parameters can be extracted easily from a relatively small number of positive examples. To avoid the tedious process of manually constructing the detector library, we introduce semi-supervised learning framework to build P-Net and the corresponding detectors together. Furthermore, we introduce the Contrast Boosting algorithm that forces the detectors to be as different as possible but not necessary to be non-overlapping.
The classification and learning ability of P-Nets are verified on three data sets: 1)vision tracked indoor activity data set; 2)vision tracked glucose monitor calibration data set; 3)sensor data set on simple weight-lifting exercise. Comparison with standard SCFG and HMM prove a P-Net based system is easier to construct and has a superior ability to classify complex human activity and detect anomaly.
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Ottergren, Elin. "Multiplier Sequences for Laguerre bases." Licentiate thesis, Stockholms universitet, Matematiska institutionen, 2012. http://urn.kb.se/resolve?urn=urn:nbn:se:su:diva-83391.
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Pólya and Schur completely characterized all real-rootedness preserving linear operators acting on the standard monomial basis in their famous work from 1914. The corresponding eigenvalues are from then on known as multiplier sequences. In 2009 Borcea and Br\"and\'en gave a complete characterization for general linear operators preserving real-rootedness (and stability) via the symbol. Relying heavily on these results, in this thesis, we are able to completely characterize multiplier sequences for generalized Laguerre bases. We also apply our methods to reprove the characterization of Hermite multiplier sequences achieved by Piotrowski in 2007.
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Biyikoglu, Türker, and Josef Leydold. "Largest Eigenvalues of Degree Sequences." Department of Statistics and Mathematics, WU Vienna University of Economics and Business, 2006. http://epub.wu.ac.at/148/1/document.pdf.
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We show that amongst all trees with a given degree sequence it is a ball where the vertex degrees decrease with increasing distance from its center that maximizes the spectral radius of the graph (i.e., its adjacency matrix). The resulting Perron vector is decreasing on every path starting from the center of this ball. This result it also connected to Faber-Krahn like theorems for Dirichlet matrices on trees. The above result is extended to connected graphs with given degree sequence. Here we give a necessary condition for a graph that has greatest maximum eigenvalue. Moreover, we show that the greatest maximum eigenvalue is monotone on degree sequences with respect to majorization. (author's abstract). Note: There is a more recent version of this paper available: "Graphs with Given Degree Sequence and Maximal Spectral Radius", Research Report Series / Department of Statistics and Mathematics, no. 72.Series: Research Report Series / Department of Statistics and Mathematics
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Rampersad, Narad. "Infinite Sequences and Pattern Avoidance." Thesis, University of Waterloo, 2004. http://hdl.handle.net/10012/1155.
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The study of combinatorics on words dates back at least to the beginning of the 20th century and the work of Axel Thue. Thue was the first to give an example of an infinite word over a three letter alphabet that contains no squares (identical adjacent blocks) xx. This result was eventually used to solve some longstanding open problems in algebra and has remarkable connections to other areas of mathematics and computer science as well. In this thesis we primarily study several variations of the problems studied by Thue in his work on repetitions in words, including some recent connections to other areas, such as graph theory. In Chapter 1 we give a brief introduction to the subject of combinatorics on words. In Chapter 2 we use uniform morphisms to construct an infinite binary word that contains no cubes xxx and no squares yy with |y| ≥ 4, thus giving a simpler construction than that of Dekking. We also use uniform morphisms to construct an infinite binary word avoiding all squares except 0², 1², and (01)², thus giving a simpler construction than that of Fraenkel and Simpson. We give some new enumeration results for these avoidance properties and solve an open problem of Prodinger and Urbanek regarding the perfect shuffle of infinite binary words that avoid arbitrarily large squares. In Chapter 3 we examine ternary squarefree words in more detail, and in Chapter 4 we study words w satisfying the property that for any sufficiently long subword w' of w, w does not contain the reversal of w' as a subword. In Chapter 5 we discuss an application of the property of squarefreeness to colourings of graphs. In Chapter 6 we study strictly increasing sequences (a(n))n≥0 of non-negative integers satisfying the equation a(a(n)) = dn. Finally, in Chapter 7 we give a brief conclusion and present some open problems.
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Allen, Patrick. "Multiplicities of Linear Recurrence Sequences." Thesis, University of Waterloo, 2006. http://hdl.handle.net/10012/2942.
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In this report we give an overview of some of the major results concerning the multiplicities of linear recurrence sequences. We first investigate binary recurrence sequences where we exhibit a result due to Beukers and a result due to Brindza, Pintér and Schmidt. We then investigate ternary recurrences and exhibit a result due to Beukers building on work of Beukers and Tijdeman. The last two chapters deal with a very important result due to Schmidt in which we bound the zero-multiplicity of a linear recurrence sequence of order t by a function involving t alone. Moreover we improve on Schmidt's bound by making some minor changes to his argument.
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Hurst, Elyssa. "Elgenvalues of Fibonacci-like Sequences." TopSCHOLAR®, 2001. http://digitalcommons.wku.edu/theses/668.
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The familiar Fibonacci sequence 1,1,2,3,5,8,13,... can be described by the recurrence relation x(0) = 1, x(1) = 1, x(n) = x(n-1) + x(n-2). For this relation, as n → oo, x(n+1) → 1 +√5 x(n) 2 ' which is the familiar golden ratio. This value is also the dominant eigenvalue of the above recurrence relation. In this series, we consider the dominant eigenvalue of some Fibonacci-like sequence of the form x(n) = ∑n-1/k+1 ak Zk (n-k) where the Zk's are independent random variables with Zk = {+1 with probability p - 1 with probability q, with p + q = 1, and for each k, the ak's are either 0 or 1.
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Avila, Jesús Rafael Alcántara. "Process Intensification in Distillation Sequences." 京都大学 (Kyoto University), 2012. http://hdl.handle.net/2433/161020.
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Williams, Mark, and n/a. "Spatial data from image sequences." University of Otago. Department of Computer Science, 2007. http://adt.otago.ac.nz./public/adt-NZDU20080130.131733.
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There are many existing methods for capturing three dimensional data from two dimensional images. Methods based on images captured from multiple view-points require solving the correspondence problem: establishing which points in each image represent the same points in the scene. Most attempts at solving the correspondence problem require carefully controlled lighting and reference points within the scene.
A new method captures many consecutive images to form a dense spatiotemporal volume as the camera-or scene-undergoes controlled motion. Feature points in the scene move along predictable paths within this volume. Analysing the exact motion of features determines their three dimensional position in the scene.
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Leung, Chi-ming. "Motif discovery for DNA sequences." Click to view the E-thesis via HKUTO, 2006. http://sunzi.lib.hku.hk/hkuto/record/B3859755X.
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Maxwell, Erin. "Evolution of avian ossification sequences." Thesis, McGill University, 2008. http://digitool.Library.McGill.CA:80/R/?func=dbin-jump-full&object_id=21942.
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The relative timing and sequence of events during embryonic development plays an important role in adult shape and thus in evolution. The sequence in which bones form in the developing embryo should therefore contain a component capable of revealing evolutionary history, however processes relating to ossification sequence and the sequences themselves are poorly known and rarely discussed. In this thesis, I describe the embryonic skeletal development of Meleagris gallopavo, Sterna hirundo, Somateria mollissima, Anas platyrhynchos, Cairina moschata, Dromaius novaehollandiae, Rhea americana and Struthio camelus for the first time in the scientific literature, focusing on ossification. All species exhibited intraspecific variation in ossification sequence, but the level of polymorphism present was generally quite low. Specimens collected from the wild did not show more variability in ossification sequence than those incubated under constant conditions in the lab. Dermal bones did not always ossify before endochondral bones, nor did neural-crest derived elements always form before elements derived from the paraxial mesoderm. All of this suggests that the factors controlling ossification sequence are complex, and more than one variable may play a role. In order to examine sequences in a more explicit phylogenetic context, I converted them into a form that is easily analyzed (event-pairs) and used these as characters for phylogenetic reconstruction. While this technique is plagued with problems involving logical and biological non-independence, it is an efficient tool for surveying conservation and divergence in ossification sequences at different levels of phylogenetic relatedness. I also reconstructed shifts on an accepted topology. The analysis indicates that ossification sequences are influenced by relative evolutionary reduction or expansion in element size. Reduced elements ossify late in sequence, and also temporally later, as measured by stage. Enlarged elementsLe temps de formation et la séquence d'événements du développement embryonnaire jouent un rôle important dans la forme adulte et dans l'évolution. La séquence selon laquelle les os se forment dans l'embryon devrait donc contenir des informations capables de révéler l'histoire évolutionnaire. Cependant, les facteurs qui influencent la séquence d'ossification et les séquences elles-mêmes sont mal compris et rarement étudiés. Dans cette thèse, je décris le développement squelettique embryonnaire chez Meleagris gallopavo, Sterna hirundo, Somateria mollissima, Anas platyrhynchos, Cairina moschata, Dromaius novaehollandiae, Rhea americana et Struthio camelus pour la première fois dans la littérature scientifique, en me concentrant sur l'ossification. Une variabilité intraspécifique entre les séquences d'ossification a été observée chez toutes espèces, mais le niveau de polymorphisme était généralement bas. Les spécimens d'espèces sauvages n'ont pas montré plus de variabilité dans la séquence d'ossification que ceux incubés dans les conditions constantes du laboratoire. Les os membraneux n'ossifient pas toujours avant les os de cartilage, et les os dérivés de la crête neurale ne se forment pas toujours avant les éléments dérivés du mésoderme paraxial. Ceci suggère que les facteurs qui contrôlent la séquence d'ossification sont complexes et que plus qu'une facteur peuvent y jouer un rôle. Afin d'examiner les séquences dans un contexte phylogénetique, je les ai convertis en une forme facile à analyser (‘paires d'événements') et ai utilisé les caractères de séquence d'ossification pour la reconstruction phylogénetique. Bien que cette technique présente des problèmes liés à un manque d'indépendence logique et biologique, c'est un outil efficace pour examiner la conservation et la divergence des séquences d'ossification à différents niveaux de rélation phylogénetique. J'ai aussi reconstruit les changements$
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Swart, Christine Scott. "Elliptic curves and related sequences." Thesis, Royal Holloway, University of London, 2003. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.406408.
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Shapiro, Larry Saul. "Affine analysis of image sequences." Thesis, University of Oxford, 1993. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.358752.
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Armstrong, Martin Neil. "Self-calibration from image sequences." Thesis, University of Oxford, 1996. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.337557.
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