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Таранова, Д. В. "Шифрування з відкритим кодом. Алгоритм RSA." Thesis, Сумський державний університет, 2015. http://essuir.sumdu.edu.ua/handle/123456789/43423.
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Chatterjee, Aakriti. "Development of an RSA Algorithm using Reduced RISC V instruction Set." University of Cincinnati / OhioLINK, 2021. http://rave.ohiolink.edu/etdc/view?acc_num=ucin1617104502129937.
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Романюк, О. О., and М. П. Смаглюк. "Програмна реалізація алгоритму шифрування RSA." Thesis, Сумський державний університет, 2017. http://essuir.sumdu.edu.ua/handle/123456789/64443.
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Криптографічні системи з відкритим ключем в даний час широко
застосовуються в різних мережевих протоколах. Асиметричне
шифрування на основі відкритого ключа RSA (розшифровується, як
Rivest, Shamir and Aldeman - творці алгоритму) використовує більшість
продуктів на ринку інформаційної безпеки. Його криптостійкість
грунтується на складності розкладання великих чисел на множники.
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Дяченко, Є., М. Кір'ян, and С. Танський. "Реалізація алгоритму RSA з використанням новітніх WEB-технологій." Thesis, Сумський державний університет, 2015. http://essuir.sumdu.edu.ua/handle/123456789/43353.
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Розвиток WEB-технологій має передове значення у розвитку науки, адже в наш час саме Інтернет є основним джерелом та провідником знань. Людина, яка має доступ до Інтернету, має доступ до всесвітньої бази інформації.
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Al-Tuwaijry, Fahd A. A. "Fast algorithms for implementation of public-key cryptosystems : VLSI simulation of modified algorithm to increase the speed of public-key cryptosystem (RSA) implementation." Thesis, University of Bradford, 1992. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.282982.
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Průcha, Jan. "Elektronický geocaching." Master's thesis, Vysoké učení technické v Brně. Fakulta elektrotechniky a komunikačních technologií, 2013. http://www.nusl.cz/ntk/nusl-220208.
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The master’s thesis is focusing on electronization of worldwide known game geocaching. It contains introduction to classic geocashing, analysis of current status and outline of possible solution. The design of electronization is based on smart card Gemalto. Very important part of the thesis is cryptographic security, therefore there is explanation of symetric and asymetric cryptography. The digital signature of transmitted message is realized by RSA algorithm, which is supported by the Gemalto smart card. Due to future expandability, it is appropriate to use general protocol. For this reason was chosen the ACP protocol which the supervisor of thesis adviced. In the following part, there is introduction to smart cards, their types and detailed description of Gemalto smart card. In the chapter 7 starts the solution of this issue and there are described the programmed apps.
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Nwaokocha, Martyns. "Shorův algoritmus v kvantové kryptografii." Master's thesis, Vysoké učení technické v Brně. Fakulta strojního inženýrství, 2021. http://www.nusl.cz/ntk/nusl-445457.
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Kryptografie je velmi důležitým aspektem našeho každodenního života, protože poskytuje teoretický základ informační bezpečnosti. Kvantové výpočty a informace se také stávají velmi důležitou oblastí vědy kvůli mnoha aplikačním oblastem včetně kryptologie a konkrétněji v kryptografii veřejných klíčů. Obtížnost čísel do hlavních faktorů je základem některých důležitých veřejných kryptosystémů, jejichž klíčem je kryptosystém RSA . Shorův kvantový faktoringový al-goritmus využívá zejména kvantový interferenční účinek kvantového výpočtu k faktorovým semi-prime číslům v polynomiálním čase na kvantovém počítači. Ačkoli kapacita současných kvantových počítačů vykonávat Shorův algoritmus je velmi omezená, existuje mnoho rozsáhlých základních vědeckých výzkumů o různých technikách optimalizace algoritmu, pokud jde o faktory, jako je počet qubitů, hloubka obvodu a počet bran. v této práci jsou diskutovány, analyzovány a porovnávány různé varianty Shorova factoringového algoritmu a kvantových obvodů. Některé varianty Shorova algoritmu jsou také simulované a skutečně prováděné na simulátorech a kvantových počítačích na platformě IBM QuantumExperience. Výsledky simulace jsou porovnávány z hlediska jejich složitosti a míry úspěšnosti. Organizace práce je následující: Kapitola 1 pojednává o některých klíčových historických výsledcích kvantové kryptografie, uvádí problém diskutovaný v této práci a představuje cíle, kterých má být dosaženo. Kapitola 2 shrnuje matematické základy kvantového výpočtu a kryptografie veřejných klíčů a popisuje notaci použitou v celé práci. To také vysvětluje, jak lze k rozbití kryptosystému RSA použít realizovatelný algoritmus pro vyhledávání objednávek nebo factoring. Kapitola 3 představuje stavební kameny Shorova algoritmu, včetně kvantové Fourierovy transformace, kvantového odhadu fází, modulární exponentiace a Shorova algoritmu. Zde jsou také uvedeny a porovnány různé varianty optimalizace kvantových obvodů. Kapitola 4 představuje výsledky simulací různých verzí Shorova algoritmu. V kapitole 5 pojednejte o dosažení cílů disertační práce, shrňte výsledky výzkumu a nastíňte budoucí směry výzkumu.
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Popovský, Michal. "Útoky postranními kanály." Master's thesis, Vysoké učení technické v Brně. Fakulta elektrotechniky a komunikačních technologií, 2009. http://www.nusl.cz/ntk/nusl-218182.
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It is very difficult in real-time breaking the cryptographic algorithms used at present. The Classical cryptoanalysis is based on finding weaknesses in the mathematical structure of the algorithm. Discovery of side channels caused a substantial change in this science. Side-channel attacks are based on incorrect physical implementation of cryptographic algorithms. This new way attack changes notions about cryptography and security of systems. This master´s thesis contains a detailed description of the whole problem of side channels and deals with side-channel attacks on the RSA asymmetric algorithm. This thesis includes the design and realization of laboratory exercise, which is focused on the time attack on the RSA algorithm implementation.
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Zeitoun, Rina. "Méthodes algébriques pour l'analyse de sécurité des implantations d'algorithmes cryptographiques." Thesis, Paris 6, 2015. http://www.theses.fr/2015PA066310/document.
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Le 10ème problème de Hilbert, consistant à trouver les solutions entières d'équations polynomiales est un problème crucial en cryptanalyse. Si ce dernier a été prouvé indécidable, Coppersmith publia en 1996 une méthode basée sur la réduction de réseaux permettant de trouver efficacement l'ensemble des petites solutions de certaines équations polynomiales. De nombreuses applications de cette méthode ont vu le jour dans le domaine de la cryptanalyse à clé publique, notamment lorsque le cryptosystème est exécuté sur un système embarqué et qu'une partie de la clé secrète est dévoilée par la réalisation d'attaques physiques sur le dispositif. Dans ce contexte, nous proposons une attaque physique sur le schéma de signature RSA en mode CRT où une application de la méthode de Coppersmith permet de compléter l'information obtenue par l'attaque physique. Nous proposons également un nouvel algorithme déterministe basé sur la méthode de Coppersmith pour factoriser les entiers de la forme $N=p^rq^s$ en temps polynomial lorsque $r$ ou $s$ sont suffisamment grands. Enfin, si les applications de la méthode de Coppersmith sont nombreuses, en pratique, du fait que les réseaux à réduire soient gigantesques, les petites solutions ne peuvent être retrouvées que jusqu'à une borne qui est plus petite que la borne théorique annoncée. Aussi, une autre contribution de cette thèse consiste en la proposition de deux méthodes permettant une accélération du temps d'exécution de l'algorithme de Coppersmith. Lorsque les deux méthodes sont combinées, le nouvel algorithme s'effectue des centaines de fois plus rapidement pour des paramètres typiques, permettant ainsi dans de nombreux cas d'atteindre la borne théoriqueThe 10th Hilbert problem, which consists in finding integer solutions to polynomial equations is a crucial problem in cryptanalysis, which has been proven to be undecidable. However, Coppersmith published in 1996 a method based on lattice reduction, which allows to efficiently find all small solutions to some polynomial equations. Many applications of this method have risen in public key cryptanalysis, especially when the cryptosystem is executed on embedded systems and part of the secret key is revealed through physical attacks performed on the device. In this context, we propose in this thesis a physical attack on the RSA signature scheme when the CRT mode is used, where an application of Coppersmith's method allows to complete the information previously obtained by the physical attack. We also propose a new deterministic algorithm based on Coppersmith's method for factoring integers of the form $N=p^rq^s$ in polynomial time, under the condition that $r$ and/or $s$ are sufficiently large.Finally, if the applications of Coppersmith's method are numerous, in practice, since the lattices to be reduced are huge, the small solutions can only be recovered until a bound which is smaller than the enounced theoretical bound. Thus, another contribution of this thesis lies in the proposition of two methods which allow to speed up the execution time of Coppersmith's algorithm. When both speedups are combined, the new algorithm performs hundreds of times faster for typical parameters, which allows to reach the theoretical bound in many cases
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Alzaabi, Mohamed Abdulla Hasan Saif. "New cryptanalysis and modelling for wireless networking." Thesis, University of Hertfordshire, 2015. http://hdl.handle.net/2299/17115.
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High data rates and interoperability of vender devices have made WiMAX a prime desire for use worldwide. WiMAX is based on the IEEE 802.16 standard. IEEE 802.16a, b, c & d versions were updated within three years of the first launch of WiMAX. However, during those early years reports were published that highlighted the security weaknesses of the standard. These weaknesses prompted the IEEE to issue a new version, 802.16e to tackle the security issues. Despite this security enhancement, WiMAX remains vulnerable. This research project looks at the vulnerability of WiMAX 802.16e Subscriber Station/Mobile Station authentication at the initial entry and proposes approaches to the prevention of Denial of Service (DoS) attacks at this point in order to secure the Media Access Control (MAC) layer from such threats. A new protocol has been designed and developed to provide confidentiality, authentication and integrity to WiMAX users. This new protocol is integrated with Z algorithm (an algorithm described later in this paper) to provide: • Confidentiality of management messages • Message Authentication code • ID to provide for message integrity and user authentication. A simulation package was also required, to prove that a linear load of DoS attack would disable or exhaust the capacity of the base station of a WiMAX network, as well as providing other simulation functions. The freely available simulation tool NIST (NIST IPSec (Internet Protocol Security) and IKE (Internet Key Exchange) Simulation) is oriented towards fixed network communications (NIIST, 2003). There are no other relevant simulation tools; hence the purpose of this research project is to develop a new tool to simulate WiMAX security vulnerabilities and test the new protocol.
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Beran, Martin. "Elektronická podatelna VUT 2." Master's thesis, Vysoké učení technické v Brně. Fakulta informačních technologií, 2007. http://www.nusl.cz/ntk/nusl-412777.
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This dissertation thesis attends to problems of electronic registry for VUT. It deals with the principal of electronic registry functioning, electronic signature and it compares offer of the commercial registries. It goes in for the proposal and implementation of the electronic registry for VUT. Since the using of the e- registry on all public service Office was legalized the people can avoid long queues and the employees are avoided from the stress before dead lines. By the communication through the electronic registry is very important the electronical signature. It is almost a full-valued and lawful alternative to the physical signature. For its safety and utility this system employes asymmetric codes and hash algorithm. Presently in many states, where the electronical signature is legalized it is used together with standard X 509 which defines the format of certificates, organization and action of certification authorities. The certification autority ensures safe connection of the person and general key for using of the electronical signature.
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Lourenço, André Luiz Ferraz. "Técnicas de proteção e restauração em redes ópticas elásticas." Universidade de São Paulo, 2015. http://www.teses.usp.br/teses/disponiveis/18/18155/tde-28012016-080915/.
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As redes ópticas estão passando por mudanças significativas, impulsionadas pelo crescimento exponencial do tráfego, principalmente advindo de serviços multimídia e armazenamento em nuvem. Esta demanda exigirá aumento da capacidade da taxa de transmissão para padrões como 400 Gb/s e 1 Tb/s. Nesse contexto, foi proposta uma arquitetura de rede com grade de frequências granular flexível chamada elastic optical network (EON). A EON divide o espectro de frequências em fatias (slots) de tamanho fixo e aloca grupos de slots contíguos estritamente de acordo com os requisitos de banda das demandas de conexão, implicando eficiência de uso do espectro. Com o aumento significativo da taxa de transmissão, acentuou-se a preocupação em manter a sobrevivência da rede, já que pouco tempo de queda no serviço pode acarretar uma imensa perda de dados. Neste trabalho, investigamos esquemas de proteção baseados em caminhos compartilhados (shared-path protection, SPP) e esquemas de restauração de tráfego. Avaliamos esquemas divulgados na literatura como o dynamic load balancing shared-path protection (DLBSPP) e esquemas de restauração como o traffic aware restoration (TAR) e bandwidth squeezed restoration (BSR). Avaliamos também uma heurística de alocação de slots chamada inverted dual stack (IDS). O DLBSPP utiliza balanceamento dinâmico de carga para computar os caminhos primários e de proteção compartilhados. O TAR executa a restauração dinâmica ordenando as conexões por granularidade de banda. O BSR utiliza a capacidade de contração de banda do EON para restaurar conexões por meio da política de melhor esforço ou de banda garantida, dependendo do acordo de níveis de serviço do cliente. O esquema IDS concentra o maior número possível de slots compartilhados em uma região do espectro. As medidas de desempenho dos algoritmos são avaliadas segundo as métricas: probabilidade de bloqueio, taxa de utilização do espectro, número médio de hops e taxa de restauração falha. As simulações computacionais mostram o bom desempenho da utilização do esquema IDS com DLBSPP.Optical networks are undergoing significant changes driven by the exponentially growing traffic, especially coming from multimedia and cloud storage services. This demand will require increasing of the transmission rate capacity as high as 400 Gb/s and 1 Tb/s. Within this context, it was proposed the elastic optical network (EON), which is a network architecture with flexible granular frequency grid. EON divides the frequency spectrum into slices (slots) of fixed size and allocates groups of contiguous slots strictly according to the bandwidth requirement of the connection demands, providing high spectrum use efficiency. The significant increase in transmission rate put emphasis on the need to maintain the survival of the network, since the occurrence of faults in the network nodes or links can cause huge loss of data. In this work, we investigate protection schemes based on shared-path protection (SPP) and traffic restoration schemes. We evaluate schemes related in the literature, such as the dynamic load balancing shared-path protection (DLBSPP), and restoration schemes such as the traffic aware restoration (TAR) and the bandwidth squeezed restoration (BSR). The DLBP scheme uses dynamic load balancing to compute primary and shared protection paths. The TAR performs dynamic restoration ordering the connections based on band granularity. The BSR uses EON\'s band squeezing feature to restore connections by means of the best effort or guaranteed bandwidth strategy, depending on the customer\'s service level agreement. IDS scheme concentrates the maximum possible number of shared slots in a given region of the spectrum. Performance of the algorithms are evaluated according to metrics: blocking probability, spectrum utilization rate, average number of hops and failure restoration rate. Computer simulations show that the use of the IDS scheme improves the performance of the investigated algorithms.
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Walker, Simon N. "High speed algorithms and architectures for RSA encryption." Thesis, University of Sheffield, 1998. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.298054.
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Schnall-Levin, Michael (Michael Benjamin). "RNA : algorithms, evolution and design." Thesis, Massachusetts Institute of Technology, 2011. http://hdl.handle.net/1721.1/67718.
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Thesis (Ph. D.)--Massachusetts Institute of Technology, Dept. of Mathematics, 2011.This electronic version was submitted by the student author. The certified thesis is available in the Institute Archives and Special Collections.
Cataloged from student submitted PDF version of thesis.
Includes bibliographical references (p. 205-214).
Modern biology is being remade by a dizzying array of new technologies, a deluge of data, and an increasingly strong reliance on computation to guide and interpret experiments. In two areas of biology, computational methods have become central: predicting and designing the structure of biological molecules and inferring function from molecular evolution. In this thesis, I develop a number of algorithms for problems in these areas and combine them with experiment to provide biological insight. First, I study the problem of designing RNA sequences that fold into specific structures. To do so I introduce a novel computational problem on Hidden Markov Models (HMMs) and Stochastic Context Free Grammars (SCFGs). I show that the problem is NP-hard, resolving an open question for RNA secondary structure design, and go on to develop a number of approximation approaches. I then turn to the problem of inferring function from evolution. I develop an algorithm to identify regions in the genome that are serving two simultaneous functions: encoding a protein and encoding regulatory information. I first use this algorithm to find microRNA targets in both Drosophila and mammalian genes and show that conserved microRNA targeting in coding regions is widespread. Next, I identify a novel phenomenon where an accumulation of sequence repeats leads to surprisingly strong microRNA targeting, demonstrating a previously unknown role for such repeats. Finally, I address the problem of detecting more general conserved regulatory elements in coding DNA. I show that such elements are widespread in Drosophila and can be identified with high confidence, a result with important implications for understanding both biological regulation and the evolution of protein coding sequences.
by Michael Schnall-Levin.
Ph.D.
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Ding, Yang. "Parametric RNA Partition Function Algorithms." Thesis, Boston College, 2010. http://hdl.handle.net/2345/1813.
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Thesis advisor: Peter CloteIn addition to the well-characterized messenger RNA, transfer RNA and ribosomal RNA, many new classes of noncoding RNA(ncRNA) have been discovered in the past few years. ncRNA has been shown to play important roles in multiple regulation and development processes. The increasing needs for RNA structural analysis software provide great opportunities on computational biologists. In this thesis I present three highly non-trivial RNA parametric structural analysis algorithms: 1) RNAhairpin and RNAmultiloop, which calculate parition functions with respect to hairpin number, multiloop number and multiloop order, 2) RNAshapeEval, which is based upon partition function calculation with respect to a fixed abstract shape, and 3) RNAprofileZ, which calculates the expected partition function and ensemble free energy given an RNA position weight matrix.I also describe the application of these software in biological problems, including evaluating purine riboswitch aptamer full alignment sequences to adopt their consensus shape, building hairpin and multiloop profiles for certain Rfam families, tRNA and pseudoknotted RNA secondary structure predictions. These algorithms hold the promise to be useful in a broad range of biological problems such as structural motifs search, ncRNA gene finders, canonical and pseudoknotted secondary structure predictions
Thesis (MS) — Boston College, 2010
Submitted to: Boston College. Graduate School of Arts and Sciences
Discipline: Biology
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Michalik, Juraj. "Non-redundant sampling in RNA Bioinformatics." Thesis, Université Paris-Saclay (ComUE), 2019. http://www.theses.fr/2019SACLX009/document.
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Un échantillonnage statistique est central à de nombreuses méthodes algorithmiques pour la bioinformatique structurale des ARNs, où ils sont couramment utilisés pour identifier des modèles structuraux importants, fournir des résumés des espaces de repliement ou approcher des quantités d'intérêt dans l'équilibre thermodynamique. Dans tous ces exemples, la redondance dans l'ensemble échantillonné est non-informative et inefficace, limitant la portée des applications des méthodes existantes. Dans cette thèse, nous introduisons le concept de l'échantillonnage non-redondante et nous explorons ses applications et conséquences en bioinformatique des ARN.Nous commençons par introduire formellement le concept d'échantillonnage non-redondante et nous démontrons que tout algorithme échantillonnant dans la distribution de Boltzmann peut être modifié en une version non-redondante. Son implémentation repose sur une structure de données spécifique et la modification d'une remontée stochastique pour fournir l'ensemble des structures uniques, avec la même complexité.Nous montrons alors une exemple pratique en implémentant le principe d'échantillonnage non-redondant au sein d'un algorithme combinatoire qui échantillonne des structures localement optimales. Nous exploitons cet outil pour étudier la cinétique des ARN, modélisant des espaces de repliement générés à partir des structures localement optimales. Ces structures agissent comme des pièges cinétiques, rendant leur prise en compte essentielle pour analyser la dynamique des ARN. Des résultats empirique montrent que des espaces de repliement générés à partir des échantillons non-redondants sont plus proches de la réalité que ceux obtenus par un échantillonnage classique.Nous considérons ensuite le problème du calcul efficace d'estimateurs statistiques à partir d'échantillons non redondants. L'absence de la redondance signifie que l'estimateur naïf, obtenu en moyennant des quantités observés dans l'échantillon, est erroné. Par contre, nous établissons un estimateur non-trivial non-biaisé spécifique aux échantillons non-redondants suivant la distribution de Boltzmann. Nous montrons que l'estimateur des échantillons non-redondants est plus efficace que l'estimateur naïf, notamment dans les cas où la majorité des l'espace de recherche est échantillonné.Finalement, nous introduisons l'algorithme d'échantillonnage, avec sa contre-partie non-redondante, pour des structures secondaires présentant des pseudonoeuds de type simple. Des pseudonoeuds sont typiquement omis pour des raisons d'efficacité, bien que beaucoup d'entre eux possèdent une grande importance biologique. Nos commençons par proposer une schéma de programmation dynamique qui permet d'énumérer tous les pseudonoeuds composés de deux hélices pouvant contenir des bases non-appariés qui s'entrecroisent. Ce schéma généralise la proposition de Reeders et Giegerich, choisi pour sa base complexité temporelle et spatiale. Par la suite, nous expliquons comment adapter cette décomposition à un algorithme d'échantillonnage statistique pour des pseudonoeuds simples. Finalement, nous présentons des résultats préliminaires et nous discutons sur l'extension de principe non-redondant dnas ce contexte.Le travail présenté dans cette thèse ouvre non seulement la porte à l'analyse cinétique des séquences d'ARN plus longues, mais aussi l'analyse structurale plus détaillée des séquences d'ARN en général. L'échantillonnage non-redondant peut être employé pour analyser des espaces de recherche pour des problèmes combinatoires susceptibles à l'échantillonnage statistique, y inclus virtuellement tous problèmes solvables par la programmation dynamique. Les principes d'échantillonnage non-redondant sont robustes et typiquement faciles à implémenter, comme démontré par l'inclusion d'échantillonnage non-redondant dans les versions récentes de Vienna package populaireSampling methods are central to many algorithmic methods in structural RNA bioinformatics, where they are routinely used to identify important structural models, provide summarized pictures of the folding landscapes, or approximate quantities of interest at the thermodynamic equilibrium.In all of these examples, redundancy within sampled sets is uninformative and computationally wasteful, limiting the scope of application of existing methods.In this thesis, we introduce the concept of non-redundant sampling, and explore its applications and consequences in RNA bioinformatics.We begin by formally introducing the concept of non-redundant sampling and demonstrate that any algorithm sampling in Boltzmann distribution can be modified into non-redundant variant. Its implementation relies on a specific data structure and a modification of the stochastic backtrack to return the set of unique structures, with the same complexity.We then show a practical example by implementing the non-redundant principle into a combinatorial algorithm that samples locally optimal structures. We use this tool to study the RNA kinetics by modeling the folding landscapes generated from sets of locally optimal structures. These structures act as kinetic traps, influencing the outcome of the RNA kinetics, thus making their presence crucial. Empirical results show that the landscapes generated from the non-redundant samples are closer to the reality than those obtained by classic approaches.We follow by addressing the problem of the efficient computation of the statistical estimates from non-redundant sampling sets. The absence of redundancy means that the naive estimator, obtained by averaging quantities observed in a sample, is erroneous. However we establish a non-trivial unbiased estimator specific to a set of unique Boltzmann distributed secondary structures. We show that the non-redundant sampling estimator performs better than the naive counterpart in most cases, specifically where most of the search space is covered by the sampling.Finally, we introduce a sampling algorithm, along with its non-redundant counterpart, for secondary structures featuring simple-type pseudoknots. Pseudoknots are typically omitted due to complexity reasons, yet many of them have biological relevance. We begin by proposing a dynamic programming scheme that allows to enumerate all recursive pseudoknots consisting of two crossing helices, possibly containing unpaired bases. This scheme generalizes the one proposed by Reeders and Giegerich, chosen for its low time and space complexities. We then explain how to adapt this decomposition into a statistical sampling algorithm for simple pseudoknots. We then present preliminary results, and discuss about extensions of the non-redundant principle in this context.The work presented in this thesis not only opens the door towards kinetics analysis for longer RNA sequences, but also more detailed structural analysis of RNAs in general. Non-redundant sampling can be applied to analyze search spaces for combinatorial problems amenable to statistical sampling, including virtually any problem solved by dynamic programming. Non-redundant sampling principles are robust and typically easy to implement, as demonstrated by the inclusion of non-redundant sampling in recent versions of the popular Vienna package
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Çağrıcı, Gökhan Koltuksuz Ahmet. "An analysis of key generation efficiency of rsa cryptos ystem in distributed environments/." [s.l.]: [s.n.], 2005. http://library.iyte.edu.tr/tezler/master/bilgisayaryazilimi/T000406.pdf.
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Thesis (Master)--İzmir Institute of Technology, İzmir, 2005.Keywords: Cryptosystem, rivest-Shamir-Adleman, parallel computing, parallel algorithms, Random number. Includes bibliographical references (leaves. 68).
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Souza, Lana Priscila. "Criptografia RSA: a teoria dos nÃmeros posta em prÃtica." Universidade Federal do CearÃ, 2015. http://www.teses.ufc.br/tde_busca/arquivo.php?codArquivo=14834.
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CoordenaÃÃo de AperfeÃoamento de Pessoal de NÃvel SuperiorDesde o advento da escrita, o envio de mensagens secretas tem sido uma importante maneira de guardar sigilo de informaÃÃes confidenciais. A arte de elaborar mensagens a partir de cÃdigos secretos surge na figura da criptografia que, com o passar do tempo, estende os seus serviÃos Ãs transaÃÃes comerciais realizadas pela internet. O principal algoritmo utilizado pela internet recebe o nome de RSA. Assim, a criptografia RSA codifica nÃmeros de cartÃes de crÃditos, senhas de bancos, nÃmeros de contas e utiliza para isso elementos de uma importante Ãrea da MatemÃtica: a Teoria dos NÃmeros.
Since the advent of writing, sending secret messages has been an important way to maintain confidentiality of sensitive information. The art of crafting messages from secret codes appears in the figure of encryption that over time extends its services to commercial transactions over the Internet. The main algorithm used by the internet is called RSA. Thus, the RSA Encryption encodes credit card numbers, bank passwords, account numbers and uses for that elements of an important area of mathematics: number theory.
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Han, Tony. "SWASAD Smith & Waterman-algorithm-specific ASIC design /." St. Lucia, Qld, 2001. http://www.library.uq.edu.au/pdfserve.php?image=thesisabs/absthe16391.pdf.
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Muñoz, Vildósola Caterina. "Implementación de un algoritmo distribuido de generación de claves RSA con umbral." Tesis, Universidad de Chile, 2016. http://repositorio.uchile.cl/handle/2250/143565.
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Ingeniera Civil en ComputaciónLa presente memoria detalla el proceso de implementación de un algoritmo distribuido de generación de claves RSA umbral. RSA es un sistema criptográfico de clave privada. Esto significa que se requieren dos claves distintas para realizar las operaciones criptográficas: una privada y una pública. En un sistema RSA la clave privada consiste en un valor privado (llamado exponente de firma o desencriptación) mientras que la clave pública consiste en dos valores (el exponente de verificación o encriptación, más un valor denominado módulo ). En un sistema RSA tanto el exponente privado como la factorización del módulo deben mantener secretos para garantizar la seguridad. En RSA umbral, la operación privada está distribuida entre n nodos. De los n nodos mencionados, se requieren t para poder realizar una operación criptográfica privada de manera exitosa. Dado que la operación privada está distribuida, la clave privada también debe estarlo. Además, tanto la claves privadas como la factorización del módulo RSA deben seguir siendo secretos. Dado lo anterior, al momento de generar las claves ningún nodo debe tomar conocimiento ni de las claves privadas ajenas, ni de la factorización del módulo RSA. El trabajo de esta memoria consistió en implementar el algoritmo de generación distribuida de claves RSA umbral propuesto por D. Boneh y M. Franklin. Dicho algoritmo logra generar un módulo RSA y un conjunto de claves privadas umbral sin que ningún nodo obtenga información sobre la factorización del módulo ni sobre las claves ajenas. A diferencia de trabajos previos, el algoritmo logra lo anterior sin requerir de un actor confiable que genere y distribuya las claves. Cabe destacar que el tiempo de ejecución del algoritmo es aleatorizado, por lo que no se puede predecir cuánto tomará en ejecutarse. A pesar de lo anterior, hay un tiempo de ejecución esperado. Se realizaron pruebas que comprobaron que la implementación estaba correcta y se comportaba de acuerdo a lo especificado en el algoritmo original. Además, se pudo comprobar que el promedio de los tiempos de ejecución medidos fueron menores al tiempo de ejecución esperado.
Este trabajo ha sido parcialmente financiado por Nic Chile Research Labs
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Gillsjö, Lukas. "Using OpenCL to Implement Median Filtering and RSA Algorithms : Two GPGPU Application Case Studies." Thesis, Linköpings universitet, Programvara och system, 2015. http://urn.kb.se/resolve?urn=urn:nbn:se:liu:diva-115786.
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Graphics Processing Units (GPU) and their development tools have advanced recently, and industry has become more interested in using them. Among several development frameworks for GPU(s), OpenCL provides a programming environment to write portable code that can run in parallel. This report describes two case studies of algorithm implementations in OpenCL. The first algorithm is Median Filtering which is a widely used image processing algorithm. The other algorithm is RSA which is a popular algorithm used in encryption. The CPU and GPU implementations of these algorithms are compared in method and speed. The GPU implementations are also evaluated by efficiency, stability, scalability and portability. We find that the GPU implementations perform better overall with some exceptions. We see that a pure GPU solution is not always the best and that a hybrid solution with both CPU and GPU may be to prefer in some cases.
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Jabbari, Hosna. "Algorithms for prediction of RNA pseudoknotted secondary structures." Thesis, University of British Columbia, 2015. http://hdl.handle.net/2429/52396.
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RNA molecules are crucial in different levels of cellular function, and their functions largely depend on their structures. Since experimental methods for determining RNA structure are expensive, computational methods for prediction of RNA secondary structure (the set of base pairs) are valuable. One such approach is based on the Minimum Free Energy (MFE) folding hypothesis, which states an RNA molecule folds into the structure with the minimum free energy. Another approach is based on the hierarchical folding hypothesis, which posits that an RNA molecule first folds into a psuedoknot- free structure (i.e., no crossing base pairs), then additional base pairs are added that may form pseudoknots (structures with crossing base pairs) to lower the structure’s free energy.
The overarching goal of this thesis is to overcome some limitations of the previous methods, namely (1) slow running time, (2) poor prediction accuracy (i.e., low number of correctly predicted base pairs), (3) limited in types of pseudoknots they can predict, and (4) limited opportunity to provide structural information that can guide prediction. We propose two algorithms and study different variations of each method. We propose a relaxed version of the hierarchical folding hypothesis and present Iterative HFold, which is based on this hypothesis. Furthermore, we propose the CCJ algorithm, an MFE-based algorithm that significantly expands the structures handled in O(n⁵) time. Employing a sparsification technique, we propose a sparse version of CCJ that improves its space usage.
While CCJ’s and Iterative HFold’s performance are not significantly different on our large data set, Iterative HFold is considerably less expensive to run than CCJ. In addition, Iterative HFold provides the user with ability to incorporate structural information as input constraint. Both CCJ and Iterative HFold predict significantly more accurate structures on key data sets than two of the best performing computational methods currently available (i.e., HotKnots V2.0 and IPknot). Of the folding hypotheses that we have studied, it seems that the relaxed hierarchical folding hypothesis has better potential to predict RNA secondary structure, at least with respect to the energy model used in this work.Science, Faculty of
Computer Science, Department of
Graduate
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Liu, Xinyi, and 刘欣怡. "A general RNA secondary structure algorithm with vertical tree grammar." Thesis, The University of Hong Kong (Pokfulam, Hong Kong), 2013. http://hdl.handle.net/10722/196439.
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Our understanding of the functions played by RNA molecules is expanded with the understanding of RNA structures. Except for primary structure, RNA molecules present pairings within a sequence, which is called RNA secondary structure. Since its discovery, RNA secondary structure has drawn considerable attention because it is widely appeared.
Many programs for RNA secondary structure prediction have been developed, including [4, 20, 38, 39, 46]. Based on our knowledge, however, there is a family of RNA secondary structure which can not be covered by any of these algorithms. And even without considering this family, none of programs can cover all other structures in Rfam data-set. These structures are found to be important in many biological processes, for example, chromosome maintenance, RNA processing, protein biosynthesis. And efficient structure prediction can give direction for experimental investigations. Here, we present a general algorithm with a new grammar: Vertical Tree Grammar (VTG) which has stochastic context-free grammar architecture for RNA secondary structure prediction. VTG significantly expands the class of structures that can be handled, including all structures that can be covered by other paper, and all structures in Rfam data-set. Our algorithm runs in O(n^6) time, and it's precision is reasonable high, with average sensitivity and specificity over
70%.published_or_final_version
Computer Science
Master
Master of Philosophy
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Reimann, Axel. "Evolutionary algorithms and optimization." Doctoral thesis, [S.l. : s.n.], 2002. http://deposit.ddb.de/cgi-bin/dokserv?idn=969093497.
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Joseph, George. "Design and implementation of high-speed algorithms for public-key cryptosystems." Diss., Pretoria : [s.n.], 2005. http://upetd.up.ac.za/thesis/available/etd-06092005-122043.
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Huang, Xiaolan. "BIOINFORMATICS INVESTIGATION OF RNA PSEUDOKNOTS." OpenSIUC, 2017. https://opensiuc.lib.siu.edu/dissertations/1463.
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Pseudoknots are a special kind of RNA structures that play functional roles in a wide variety of biological processes. Pseudoknots are best known for their involvement in the −1 programed ribosomal frameshifting (−1 PRF) and stop codon readthrough translational recoding events as the stimulatory structures. In this dissertation, three large scale bioinformatics investigations were carried out on the roles of pseudoknots in the −1 PRF, as well as stop codon readthrough, recoding mechanisms in viral and human mRNAs. To meet the specific needs of the bioinformatics investigations, a new algorithm and method for the detection of RNA pseudoknots has been developed. The new approach differs from all existing pseudoknot detection programs in that it is capable of identifying all potential pseudoknots in any given RNA sequence with no length limitation, in a time efficient manner. This capability is essential for large scale applications in which large datasets of long RNA sequences are analyzed. The algorithm and method have been implemented, with different flavors, in three large scale sequence analysis investigations. The three datasets of mRNA sequences are: 1) full-length genomic mRNA sequences of all animal viruses known or expected to use the −1 PRF and stop codon readthrough recoding mechanisms for viral protein production; 2) full-length genomic mRNA sequences of 4000 plus different strains of human immunodeficiency virus type-1 (HIV-1); 3) 34,000 plus full-length human mRNA sequences. Results from systematic sequence analysis on these three datasets prove the usefulness and robustness of the newly developed pseudoknot detection approach. A large number of previously unknown potential pseudoknots were detected in the viral and human mRNA sequences under investigation. Post detection analysis leads to new mechanistic insights and hypotheses of pseudoknot dependent translational recoding. Some unifying themes of RNA pseudoknot structures in general are also uncovered. The results provide solid basis for further experimental and bioinformatics studies in the future.
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Wang, Xueyi Snoeyink Jack. "Exploring RNA and protein 3D structures by geometric algorithms." Chapel Hill, N.C. : University of North Carolina at Chapel Hill, 2008. http://dc.lib.unc.edu/u?/etd,1905.
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Thesis (Ph. D.)--University of North Carolina at Chapel Hill, 2008.Title from electronic title page (viewed Dec. 11, 2008). "... in partial fulfillment of the requirements for the degree of Doctor of Philosophy in the Department of Computer Science." Discipline: Computer Science; Department/School: Computer Science.
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Chang, Ding-chen. "Underwater acoustic pulse propagation using the Recursive Ray Acoustics (RRA) Algorithm." Thesis, Monterey, Calif. : Springfield, Va. : Naval Postgraduate School ; Available from National Technical Information Service, 1995. http://handle.dtic.mil/100.2/ADA303441.
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Mathuriya, Amrita. "Prediction of secondary structures for large RNA molecules." Thesis, Atlanta, Ga. : Georgia Institute of Technology, 2009. http://hdl.handle.net/1853/28195.
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Thesis (M. S.)--Computing, Georgia Institute of Technology, 2009.Committee Chair: Bader, David; Committee Co-Chair: Heitsch, Christine; Committee Member: Harvey, Stephen; Committee Member: Vuduc, Richard.
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Mangul, Serghei. "Algorithms for Transcriptome Quantification and Reconstruction from RNA-Seq Data." Digital Archive @ GSU, 2012. http://digitalarchive.gsu.edu/cs_diss/71.
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Massively parallel whole transcriptome sequencing and its ability to generate full transcriptome data at the single transcript level provides a powerful tool with multiple interrelated applications, including transcriptome reconstruction, gene/isoform expression estimation, also known as transcriptome quantification. As a result, whole transcriptome sequencing has become the technology of choice for performing transcriptome analysis, rapidly replacing array-based technologies. The most commonly used transcriptome sequencing protocol, referred to as RNA-Seq, generates short (single or paired) sequencing tags from the ends of randomly generated cDNA fragments. RNA-Seq protocol reduces the sequencing cost and significantly increases data throughput, but is computationally challenging to reconstruct full-length transcripts and accurately estimate their abundances across all cell types.
We focus on two main problems in transcriptome data analysis, namely, transcriptome reconstruction and quantification. Transcriptome reconstruction, also referred to as novel isoform discovery, is the problem of reconstructing the transcript sequences from the sequencing data. Reconstruction can be done de novo or it can be assisted by existing genome and transcriptome annotations. Transcriptome quantification refers to the problem of estimating the expression level of each transcript. We present a genome-guided and annotation-guided transcriptome reconstruction methods as well as methods for transcript and gene expression level estimation. Empirical results on both synthetic and real RNA-seq datasets show that the proposed methods improve transcriptome quantification and reconstruction accuracy compared to previous methods.
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Yu, Lu. "Using Genetic Algorithms to Calculate Floodway Stations With HEC-RAS." University of Dayton / OhioLINK, 2015. http://rave.ohiolink.edu/etdc/view?acc_num=dayton1449564866.
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Wang, Wei. "Alignement pratique de structure-séquence d'ARN avec pseudonœuds." Thesis, Université Paris-Saclay (ComUE), 2017. http://www.theses.fr/2017SACLS563/document.
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Aligner des macromolécules telles que des protéines, des ADN et des ARN afin de révéler ou exploiter, leur homologie fonctionnelle est un défi classique en bioinformatique, qui offre de nombreuses applications, notamment dans la modélisation de structures et l'annotation des génomes. Un certain nombre d'algorithmes et d'outils ont été proposés pour le problème d'alignement structure-séquence d'ARN. Cependant, en ce qui concerne les ARN complexes, comportant des pseudo-noeuds, des interactions multiples et des paires de bases non canoniques, de tels outils sont rarement utilisés dans la pratique, en partie à cause de leurs grandes exigences de calcul, et de leur incapacité à supporter des types généraux de structures. Récemment, Rinaudo et al. ont donné un algorithme paramétré général pour la comparaison structure-séquence d'ARN, qui est capable de prendre en entrée n'importe quel type de structures comportant des pseudo-noeuds. L'algorithme paramétré est un algorithme de programmation dynamique basée sur la décomposition arborescente. Nous avons développé plusieurs variantes et extensions de cet algorithme. Afin de l'accélérer sans perte sensible de précision, nous avons introduit une approche de programmation dynamique par bandes. De plus, trois algorithmes ont été développés pour obtenir des alignements sous-optimaux. De plus, nous introduisons dans ce contexte la notion de MEA (Maximum-expected Structure-Alignment) pour calculer un alignement avec la précision maximale attendue sur un ensemble d'alignements. Tous ces algorithmes ont été implémentés dans un logiciel nommé LiCoRNA (aLignment of Complex RNAs). Les performances de LiCoRNA ont été évaluées d'abord sur l'alignement des graines des familles de de la base de données RFAM qui comportent des pseudo-noeuds. Comparé aux autres algorithmes de l'état de l'art, LiCoRNA obtient généralement des résultats équivalents ou meilleurs que ses concurrents. Grâce à la grande précision démontrée par LiCoRNA, nous montrons que cet outil peut être utilisé pour améliorer les alignements de certaines familles de RFAM qui comportent des pseudo-noeudsAligning macromolecules such as proteins, DNAs and RNAs in order to reveal, or conversely exploit, their functional homology is a classic challenge in bioinformatics, with far-reaching applications in structure modelling and genome annotation. In the specific context of complex RNAs, featuring pseudoknots, multiple interactions and non-canonical base pairs, multiple algorithmic solutions and tools have been proposed for the structure sequence alignment problem. However, such tools are seldom used in practice, due in part to their extreme computational demands, and because of their inability to support general types of structures. Recently, Rinaudo et al. gave a fully general parameterised algorithm for structure-sequence comparison, which is able to take as input any type of pseudoknotted structures. The parameterised algorithm is a tree decomposition based dynamic programming. To accelerate the dynamic programming algorithm without losing two much accuracy, we introduced a banded dynamic programming. Then three algorithms are introduced to get the suboptimal structure-sequence alignments. Furthermore, we introduce the notation Maximum Expected structure-sequence Alignment (MEA) to compute an alignment with maximum expected accuracy over a set of alignments. The Boltzmann match probability are computed based on the inside-outside algorithm. The algorithms are implemented in a software named LiCoRNA (aLignment of Complex RNAs). We first evaluate the performance of LiCoRNA on the seed alignment in the pseudoknotted RFAM families. Compared to the state-of-the-art algorithms, LiCoRNA shows generally equivalent or better results than its competitors. With the high accuracy showed by LiCoRNA, we further curate RFAM full pseudoknotted alignment. The reason why we realign full alignments is that covariance model does not support pseudoknot which may lead to misalign when building the full alignment
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Darbha, Sriram. "RNA Homology Searches Using Pair Seeding." Thesis, University of Waterloo, 2005. http://hdl.handle.net/10012/1172.
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Due to increasing numbers of non-coding RNA (ncRNA) being discovered recently, there is interest in identifying homologs of a given structured RNA sequence. Exhaustive homology searching for structured RNA molecules using covariance models is infeasible on genome-length sequences. Hence, heuristic methods are employed, but they largely ignore structural information in the query. We present a novel method, which uses secondary structure information, to perform homology searches for a structured RNA molecule. We define the concept of a pair seed and theoretically model alignments of random and related paired regions to compute expected sensitivity and specificity. We show that our method gives theoretical gains in sensitivity and specificity compared to a BLAST-based heuristic approach. We provide experimental verification of this gain. We also show that pair seeds can be effectively combined with the spaced seeds approach to nucleotide homology search. The hybrid search method has theoretical specificity superior to that of the BLAST seed. We provide experimental evaluation of our hypotheses. Finally, we note that our method is easily modified to process pseudo-knotted regions in the query, something outside the scope of covariance model based methods.
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Mui, Yuen-chi. "Comparison and improvement of siRNA design tools." Click to view the E-thesis via HKUTO, 2004. http://sunzi.lib.hku.hk/hkuto/record/B30722019.
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Song, Yinglei. "Grammatical Study of Ribonucleic Acids Pseudo-Knot Structures: A Simulated Annealing Approach." Ohio : Ohio University, 2003. http://www.ohiolink.edu/etd/view.cgi?ohiou1071064106.
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Bayegan, Amir Hossein. "Novel algorithms to analyze RNA secondary structure evolution and folding kinetics." Thesis, Boston College, 2018. http://hdl.handle.net/2345/bc-ir:108256.
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Thesis advisor: Peter CloteRNA molecules play important roles in living organisms, such as protein translation, gene regulation, and RNA processing. It is known that RNA secondary structure is a scaffold for tertiary structure leading to extensive amount of interest in RNA secondary structure. This thesis is primarily focused on the development of novel algorithms for the analysis of RNA secondary structure evolution and folding kinetics. We describe a software RNAsampleCDS to generate mRNA sequences coding user-specified peptides overlapping in up to six open reading frames. Sampled mRNAs are then analyzed with other tools to provide an estimate of their secondary structure properties. We investigate homology of RNAs with respect to both sequence and secondary structure information as well. RNAmountAlign an efficient software package for multiple global, local, and semiglobal alignment of RNAs using a weighted combination of sequence and structural similarity with statistical support is presented. Furthermore, we approach RNA folding kinetics from a novel network perspective, presenting algorithms for the shortest path and expected degree of nodes in the network of all secondary structures of an RNA. In these algorithms we consider move set MS2 , allowing addition, removal and shift of base pairs used by several widely-used RNA secondary structure folding kinetics software that implement Gillespie’s algorithm. We describe MS2distance software to compute the shortest MS2 folding trajectory between any two given RNA secondary structures. Moreover, RNAdegree software implements the first algorithm to efficiently compute the expected degree of an RNA MS2 network of secondary structures. The source code for all the software and webservers for RNAmountAlign, MS2distance, and RNAdegree are publicly available at http://bioinformatics.bc.edu/clotelab/
Thesis (PhD) — Boston College, 2018
Submitted to: Boston College. Graduate School of Arts and Sciences
Discipline: Biology
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Tominaga, Sacomoto Gustavo Akio. "Efficient algorithms for de novo assembly of alternative splicing events from RNA-seq data." Phd thesis, Université Claude Bernard - Lyon I, 2014. http://tel.archives-ouvertes.fr/tel-01015506.
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In this thesis, we address the problem of identifying and quantifying variants (alternative splicing and genomic polymorphism) in RNA-seq data when no reference genome is available, without assembling the full transcripts. Based on the idea that each variant corresponds to a recognizable pattern, a bubble, in a de Bruijn graph constructed from the RNA-seq reads, we propose a general model for all variants in such graphs. We then introduce an exact method, called KisSplice, to extract alternative splicing events and show that it outperforms general purpose transcriptome assemblers. We put an extra effort to make KisSplice as scalable as possible. In order to improve the running time, we propose a new polynomial delay algorithm to enumerate bubbles. We show that it is several orders of magnitude faster than previous approaches. In order to reduce its memory consumption, we propose a new compact way to build and represent a de Bruijn graph. We show that our approach uses 30% to 40% less memory than the state of the art, with an insignificant impact on the construction time. Additionally, we apply the techniques developed to list bubbles in two classical problems: cycle enumeration and the K-shortest paths problem. We give the first optimal algorithm to list cycles in undirected graphs, improving over Johnson's algorithm. This is the first improvement to this problem in almost 40 years. We then consider a different parameterization of the K-shortest (simple) paths problem: instead of bounding the number of st-paths, we bound the weight of the st-paths. We present new algorithms using exponentially less memory than previous approaches
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Wong, king-fung, and 黃景峰. "Non-coding RNA identification along genome." Thesis, The University of Hong Kong (Pokfulam, Hong Kong), 2011. http://hub.hku.hk/bib/B4581949X.
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Cleynen, Alice. "Approches statistiques en segmentation : application à la ré-annotation de génome." Phd thesis, Université Paris Sud - Paris XI, 2013. http://tel.archives-ouvertes.fr/tel-00913851.
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Nous proposons de modéliser les données issues des technologies de séquençage du transcriptome (RNA-Seq) à l'aide de la loi binomiale négative, et nous construisons des modèles de segmentation adaptés à leur étude à différentes échelles biologiques, dans le contexte où ces technologies sont devenues un outil précieux pour l'annotation de génome, l'analyse de l'expression des gènes, et la détection de nouveaux transcrits. Nous développons un algorithme de segmentation rapide pour analyser des séries à l'échelle du chromosome, et nous proposons deux méthodes pour l'estimation du nombre de segments, directement lié au nombre de gènes exprimés dans la cellule, qu'ils soient précédemment annotés ou détectés à cette même occasion. L'objectif d'annotation précise des gènes, et plus particulièrement de comparaison des sites de début et fin de transcription entre individus, nous amène naturellement à nous intéresser à la comparaison des localisations de ruptures dans des séries indépendantes. Nous construisons ainsi dans un cadre de segmentation bayésienne des outils de réponse à nos questions pour lesquels nous sommes capable de fournir des mesures d'incertitude. Nous illustrons nos modèles, tous implémentés dans des packages R, sur des données RNA-Seq provenant d'expériences sur la levure, et montrons par exemple que les frontières des introns sont conservées entre conditions tandis que les débuts et fin de transcriptions sont soumis à l'épissage différentiel.
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Gatti, Lorenzo. "Analysis of the behaviour of the BSP algorithm on instances of random hypergraph bicoloring." Master's thesis, Alma Mater Studiorum - Università di Bologna, 2018. http://amslaurea.unibo.it/15787/.
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Nonostante la potenza e la velocità di calcolo di un moderno computer siano enormi ed in continuo sviluppo, esistono problemi particolari che richiedono tempi di computazione pari o addirittura superiori all'età dell'universo anche per i supercomputer più tecnologici. In questo contesto l'analisi delle transizioni di fase della meccanica statistica applicata ai sistemi disordinati è in grado di fornire uno scenario di studio completamente nuovo e meccaniche per lo sviluppo di algoritmi sempre più intelligenti.
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Bukvic, Ivica Ico. "Tabula Rasa." University of Cincinnati / OhioLINK, 2005. http://rave.ohiolink.edu/etdc/view?acc_num=ucin1131065629.
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Khuhro, Zain. "The development of a clique finding algorithm and its use in comparing RNA tertiary structures." Thesis, University of Essex, 2011. https://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.548592.
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Selega, Alina. "Computational methods for RNA integrative biology." Thesis, University of Edinburgh, 2018. http://hdl.handle.net/1842/29630.
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Ribonucleic acid (RNA) is an essential molecule, which carries out a wide variety of functions within the cell, from its crucial involvement in protein synthesis to catalysing biochemical reactions and regulating gene expression. Such diverse functional repertoire is indebted to complex structures that RNA can adopt and its flexibility as an interacting molecule. It has become possible to experimentally measure these two crucial aspects of RNA regulatory role with such technological advancements as next-generation sequencing (NGS). NGS methods can rapidly obtain the nucleotide sequence of many molecules in parallel. Designing experiments, where only the desired parts of the molecule (or specific parts of the transcriptome) are sequenced, allows to study various aspects of RNA biology. Analysis of NGS data is insurmountable without computational methods. One such experimental method is RNA structure probing, which aims to infer RNA structure from sequencing chemically altered transcripts. RNA structure probing data is inherently noisy, affected both by technological biases and the stochasticity of the underlying process. Most existing methods do not adequately address the issue of noise, resorting to heuristics and limiting the informativeness of their output. In this thesis, a statistical pipeline was developed for modelling RNA structure probing data, which explicitly captures biological variability, provides automated bias-correcting strategies, and generates a probabilistic output based on experimental measurements. The output of our method agrees with known RNA structures, can be used to constrain structure prediction algorithms, and remains robust to reduced sequence coverage, thereby increasing sensitivity of the technology. Another recent experimental innovation maps RNA-protein interactions at very high temporal resolution, making it possible to study rapid binding events happening on a minute time scale. In this thesis, a non-parametric algorithm was developed for identifying significant changes in RNA-protein binding time-series between different conditions. The method was applied to novel yeast RNA-protein binding time-course data to study the role of RNA degradation in stress response. It revealed pervasive changes in the binding to the transcriptome of the yeast transcription termination factor Nab3 and the cytoplasmic exoribonuclease Xrn1 under nutrient stress. This challenged the common assumption of viewing transcriptional changes as the major driver of changes in RNA expression during stress and highlighted the importance of degradation. These findings inspired a dynamical model for RNA expression, where transcription and degradation rates are modelled using RNA-protein binding time-series data.
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Mui, Yuen-chi, and 梅宛芝. "Comparison and improvement of siRNA design tools." Thesis, The University of Hong Kong (Pokfulam, Hong Kong), 2004. http://hub.hku.hk/bib/B30722019.
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Vychodil, Petr. "Softwarová podpora výuky kryptosystémů založených na problému faktorizace velkých čísel." Master's thesis, Vysoké učení technické v Brně. Fakulta elektrotechniky a komunikačních technologií, 2009. http://www.nusl.cz/ntk/nusl-218146.
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This thesis deals with new teaching software, which supports asymmetric encryption algorithms based on the issue of large numbers´ factorization. A model program was created. It allows to carry out operations related to encryption and decryption with an interactive control. There is a simple way to understand the principle of the RSA encryption method with its help. The encryption of algorithms is generally analysed in chapters 1,2. Chapters 3 and 4 deals with RSA encryption algorithm in much more details, and it also describes the principles of the acquisition, management and usage of encryption keys. Chapters 5 suggest choosing of appropriate technologies for the creation of the final software product, which allow an appropriate way to present the characteristics of the extended RSA encryption algorithm. The final software product is the java applet. Aplet is described in the chaprers 6 and 7. It is divided into a theoretical and practical part. The theoretical part presents general information about the RSA encryption algorithm. The practical part allows the users of the program to have a try at tasks connected with the RSA algorthm in their own computers. The last part of Java applet deals with the users´ work results. The information obtained by the user in the various sections of the program are satisfactory enough to understand the principle of this algorithm´s operations.
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Hu, Yin. "A NOVEL COMPUTATIONAL FRAMEWORK FOR TRANSCRIPTOME ANALYSIS WITH RNA-SEQ DATA." UKnowledge, 2013. http://uknowledge.uky.edu/cs_etds/17.
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The advance of high-throughput sequencing technologies and their application on mRNA transcriptome sequencing (RNA-seq) have enabled comprehensive and unbiased profiling of the landscape of transcription in a cell. In order to address the current limitation of analyzing accuracy and scalability in transcriptome analysis, a novel computational framework has been developed on large-scale RNA-seq datasets with no dependence on transcript annotations. Directly from raw reads, a probabilistic approach is first applied to infer the best transcript fragment alignments from paired-end reads. Empowered by the identification of alternative splicing modules, this framework then performs precise and efficient differential analysis at automatically detected alternative splicing variants, which circumvents the need of full transcript reconstruction and quantification. Beyond the scope of classical group-wise analysis, a clustering scheme is further described for mining prominent consistency among samples in transcription, breaking the restriction of presumed grouping. The performance of the framework has been demonstrated by a series of simulation studies and real datasets, including the Cancer Genome Atlas (TCGA) breast cancer analysis. The successful applications have suggested the unprecedented opportunity in using differential transcription analysis to reveal variations in the mRNA transcriptome in response to cellular differentiation or effects of diseases.
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Huang, Yan. "NOVEL COMPUTATIONAL METHODS FOR TRANSCRIPT RECONSTRUCTION AND QUANTIFICATION USING RNA-SEQ DATA." UKnowledge, 2015. http://uknowledge.uky.edu/cs_etds/28.
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The advent of RNA-seq technologies provides an unprecedented opportunity to precisely profile the mRNA transcriptome of a specific cell population. It helps reveal the characteristics of the cell under the particular condition such as a disease. It is now possible to discover mRNA transcripts not cataloged in existing database, in addition to assessing the identities and quantities of the known transcripts in a given sample or cell. However, the sequence reads obtained from an RNA-seq experiment is only a short fragment of the original transcript. How to recapitulate the mRNA transcriptome from short RNA-seq reads remains a challenging problem. We have proposed two methods directly addressing this challenge. First, we developed a novel method MultiSplice to accurately estimate the abundance of the well-annotated transcripts. Driven by the desire of detecting novel isoforms, a max-flow-min-cost algorithm named Astroid is designed for simultaneously discovering the presence and quantities of all possible transcripts in the transcriptome. We further extend an \emph{ab initio} pipeline of transcriptome analysis to large-scale dataset which may contain hundreds of samples. The effectiveness of proposed methods has been supported by a series of simulation studies, and their application on real datasets suggesting a promising opportunity in reconstructing mRNA transcriptome which is critical for revealing variations among cells (e.g. disease vs. normal).
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Höchsmann, Matthias. "The tree alignment model: algorithms, implementations and applications for the analysis of RNA secondary structures." [S.l. : s.n.], 2005. http://deposit.ddb.de/cgi-bin/dokserv?idn=97547748X.
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Tang, Shiyuyun. "Improving algorithms of gene prediction in prokaryotic genomes, metagenomes, and eukaryotic transcriptomes." Diss., Georgia Institute of Technology, 2016. http://hdl.handle.net/1853/54998.
Full textAbstract:
Next-generation sequencing has generated enormous amount of DNA and RNA sequences that potentially carry volumes of genetic information, e.g. protein-coding genes. The thesis is divided into three main parts describing i) GeneMarkS-2, ii) GeneMarkS-T, and iii) MetaGeneTack.
In prokaryotic genomes, ab initio gene finders can predict genes with high accuracy. However, the error rate is not negligible and largely species-specific. Most errors in gene prediction are made in genes located in genomic regions with atypical GC composition, e.g. genes in pathogenicity islands. We describe a new algorithm GeneMarkS-2 that uses local GC-specific heuristic models for scoring individual ORFs in the first step of analysis. Predicted atypical genes are retained and serve as ‘external’ evidence in subsequent runs of self-training. GeneMarkS-2 also controls the quality of training process by effectively selecting optimal orders of the Markov chain models as well as duration parameters in the hidden semi-Markov model. GeneMarkS-2 has shown significantly improved accuracy compared with other state-of-the-art gene prediction tools.
Massive parallel sequencing of RNA transcripts by the next generation technology (RNA-Seq) provides large amount of RNA reads that can be assembled to full transcriptome. We have developed a new tool, GeneMarkS-T, for ab initio identification of protein-coding regions in RNA transcripts. Unsupervised estimation of parameters of the algorithm makes unnecessary several steps in the conventional gene prediction protocols, most importantly the manually curated preparation of training sets. We have demonstrated that the GeneMarkS-T self-training is robust with respect to the presence of errors in assembled transcripts and the accuracy of GeneMarkS-T in identifying protein-coding regions and, particularly, in predicting gene starts compares favorably to other existing methods.
Frameshift prediction (FS) is important for analysis and biological interpretation of metagenomic sequences. Reads in metagenomic samples are prone to sequencing errors. Insertion and deletion errors that change the coding frame impair the accurate identification of protein coding genes. Accurate frameshift prediction requires sufficient amount of data to estimate parameters of species-specific statistical models of protein-coding and non-coding regions. However, this data is not available; all we have is metagenomic sequences of unknown origin. The challenge of ab initio FS detection is, therefore, twofold: (i) to find a way to infer necessary model parameters and (ii) to identify positions of frameshifts (if any). We describe a new tool, MetaGeneTack, which uses a heuristic method to estimate parameters of sequence models used in the FS detection algorithm. It was shown on several test sets that the performance of MetaGeneTack FS detection is comparable or better than the one of earlier developed program FragGeneScan.
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Sohiya, Yotsukura. "Computational Framework for the Dissection of Cancer Genomic Architecture and its Association in Different Biomarkers." 京都大学 (Kyoto University), 2016. http://hdl.handle.net/2433/217149.
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