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Tesi sul tema "Sequencer"
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1
Persson, Daniel. "Sequi : Tredimensionell sequencer." Thesis, Konstfack, Grafisk Design & Illustration, 2014. http://urn.kb.se/resolve?urn=urn:nbn:se:konstfack:diva-4707.
Testo completoAbstract (sommario):
Music production software has a strong tradition of two-dimensional graphical user interface (GUI), in which the time line is represented as a flat composition either horizontally (from left to right) or vertically (from top to bottom). In my degree work titled Sequi, I approach music composition from a different angle. Instead of a two-dimensional time line with only two possibly ways of progression (forward or backward) I constructed a three-dimensional GUI with the maximum of four different ways of progression from any given point in a composition. The height axis is used to describe time-intervals (the time between downbeats) and the wide and depth axes are used to describe progression from one sound to another.
2
Ait-Ghezala, Ahmed 1976. "Software systems for a DNA sequencer." Thesis, Massachusetts Institute of Technology, 2000. http://hdl.handle.net/1721.1/8931.
Testo completoAbstract (sommario):
Thesis (M.Eng. and S.B.)--Massachusetts Institute of Technology, Dept. of Electrical Engineering and Computer Science, 2000.<br>Includes bibliographical references (leaf 49).<br>The initiative to complete the sequencing of the human genome is bringing the need for high-throughput sequencing capabilities to the forefront. We at the BioMEMS engineering group at the Whitehead Institute are designing and building a new sequencing machine that uses a 384 glass "chip" to dramatically increase sequencing rates. This thesis describes the design and implementation of two of the machine's software components. The first is a prototype application for the control of a robot used to automate sample loading. The second is a software filter that allows us to generate quality scores from data processed by Trout using Phred. I present the algorithm used to perform the filtering and show that the results are comparable to the processing of data with the Plan- Phred processing package.<br>by Ahmed Ait-Ghezala.<br>M.Eng.and S.B.
3
Crabtree, H. John. "Development of a high throughput, multicapillary DNA sequencer." Thesis, National Library of Canada = Bibliothèque nationale du Canada, 1997. http://www.collectionscanada.ca/obj/s4/f2/dsk3/ftp04/nq21562.pdf.
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Phạm, Paul Tân Thế. "A general-purpose pulse sequencer for quantum computing." Thesis, Massachusetts Institute of Technology, 2005. http://hdl.handle.net/1721.1/32106.
Testo completoAbstract (sommario):
Thesis (M. Eng.)--Massachusetts Institute of Technology, Dept. of Electrical Engineering and Computer Science, 2005.<br>This electronic version was submitted by the student author. The certified thesis is available in the Institute Archives and Special Collections.<br>Includes bibliographical references (p. 165-170).<br>Quantum mechanics presents a more general and potentially more powerful model of computation than classical systems. Quantum bits have many physically different representations which nonetheless share a common need for modulating pulses of electromagnetic waves. This thesis presents the design and evaluates the implementation of a general-purpose sequencer which supports fast, programmable pulses; a flexible, open design; and feedback operation for adaptive algorithms. The sequencer achieves a timing resolution, minimum pulse duration, and minimum delay of 10 nanoseconds; it has 64 simultaneously-switching, independent digital outputs and 8 digital inputs for triggering or feedback. Multiple devices can operate in a daisy chain to facilitate adding and removing channels. An FPGA is used to implement a firmware network stack and a specialized pulse processor core whose modules are all interconnected using the Wishbone bus standard. Users can write pulse programs in an assembly language and control the device from a host computer over an Ethernet network. An embedded web server provides an intuitive, graphical user interface, while a non-interactive, efficient UDP protocol provides programmatic access to third-party software. The performance characteristics, tolerances, and cost of the device are measured and compared with those of contemporary research and commercial offerings. Future improvements and extensions are suggested. All circuit schematics, PCB layouts, source code, and design documents are released under an open source license.<br>by Paul Tân Thế Phạm.<br>M.Eng.
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Bay, Sue J. "The construction and evaluation of a multiple capillary DNA sequencer." Thesis, National Library of Canada = Bibliothèque nationale du Canada, 1998. http://www.collectionscanada.ca/obj/s4/f2/dsk2/ftp03/NQ34733.pdf.
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Zhu, Zhineng. "Low Noise Offset Operational Amplifier for Nanopore-based Gene Sequencer." Fogler Library, University of Maine, 2007. http://www.library.umaine.edu/theses/pdf/ZhuZ2007.pdf.
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Bowler, I. "Digital techniques in the storage and processing of audio waveforms for music synthesis." Thesis, Bucks New University, 1986. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.373583.
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Brandt, Jason J. "Fault-tolerant sequencer using FPGA-based logic designs for space applications." Thesis, Monterey, California: Naval Postgraduate School, 2013. http://hdl.handle.net/10945/38884.
Testo completoAbstract (sommario):
Approved for public release; distribution is unlimited.<br>The design of a device that controls the sequence and timing of deployment of CubeSats on the Naval Postgraduate Schools CubeSat Launcher (NPSCuL) is detailed in this thesis. This design is intended to be implemented on a field-programmable gate array (FPGA) installed into the NPSCuL. This configuration allows flexibility in reprogramming the launch sequence and adding additional functionality in future designs. Operating an FPGA on orbit presents unique challenges due to the radiation environment. Radiation from space cannot be shielded efficiently, so devices must be tolerant of the expected effects. The most common effect, the single-event upset can have detrimental effects on operating electronics, causing undesired changes to data. To combat this problem, fault tolerant techniques, such as triple-modular redundancy (TMR) are explored. In these methods, multiple redundant copies of the design are operated simultaneously, and the outputs are voted on by special circuits to eliminate errors. Comparisons between manual and software generated TMR methods are tested, and the design is implemented on test hardware for further verification. Finally, future research and testing is discussed to continue to ready the design for employment of the sequencer on an actual space mission.
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Tumati, Raghu. "Solid-State Nanopore Characterization and Low noise Transimpedance Amplifier for Nanopore-Based Gene Sequencer." Fogler Library, University of Maine, 2008. http://www.library.umaine.edu/theses/pdf/TumatiR2008.pdf.
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Goff, Jordan K. "Adaptation of a fault–tolerant FPGA–based launch sequencer as a CubeSat payload processor." Thesis, Monterey, California: Naval Postgraduate School, 2014. http://hdl.handle.net/10945/42634.
Testo completoAbstract (sommario):
Approved for public release; distribution is unlimited<br>The purpose of this thesis is to design and test a fault–tolerant reduced instruction set computer processor running a subset of the multiprocessor without interlocked pipelined stages instruction set. This processor is implemented on a field programmable gate array (FPGA) and will be used as the foundation for a payload processor on a cube satellite developed at the Naval Postgraduate School. This thesis begins by considering the radiation effects present in the space environment and the various fault– tolerant designs used to guard against specific types of particle events. The internal triple modular redundancy method is selected and implemented at each pipeline stage of the processor. Next, a target FPGA is selected based on the performance requirements of the processor. The Virtex–5 (registered trademark of Xilinx, Inc.) is selected over the ProASIC3 (registered trademark of Microsemi, Inc.) due to its enhanced capabilities and potential to support expansion for future applications. The hardware design is presented as a hybrid Verilog and schematic based design. The system consists of the processor and a universal asynchronous receiver/transmitter that reads and writes data received from a generic serial interface. The device is simulated to ensure proper logic functionality. Conclusions and future work are discussed.
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Parobek, Lucas S. "RESEARCH, DEVELOPMENT AND TESTING OF A FAULT-TOLERANT FPGA-BASED SEQUENCER FOR CUBESAT LAUNCHING APPLICATIONS." Monterey, California. Naval Postgraduate School, 2013. http://hdl.handle.net/10945/32882.
Testo completoAbstract (sommario):
This thesis concerns various means of implementing fault tolerance in logic for use in a general payload processor design. The first specific application of this research is a sequencer developed for deploying CubeSats. The sequencer shall be capable of the timing and accurate deployment of multiple CubeSats from a host spacecraft and shall have the capability for quick reconfiguration prior to launch. This research considers a variety of hardware for suitability toward sequencer construction; field programmable gate arrays (FPGAs) are chosen as the primary device. The design further evolves to selection of the Actel ProASIC3 series of FPGAs. Initial logic test configurations are implemented on a development kit with analysis of results provided. Fault-tolerant techniques are compared with a set of experiments to determine optimum resource utilization and timing schemes. Triple modular redundancy (TMR) is selected as the technique for fault-tolerant logic implementation in the sequencer. Preliminary test boards are built via schematic design and printed circuit board layout. The manufacturing, integration and testing of the ProASIC3 Test Board is fully discussed. A follow-on flight prototype board is designed with more extensive hardware allowing for implementation of fault-tolerant techniques and future growth capability. Recommendations for future work are discussed.
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Borgen, Gary. "MICROCONTROLLER BASED PCM ENCODERS FOR TELEMETRY INSTRUMENTATION." International Foundation for Telemetering, 2005. http://hdl.handle.net/10150/604920.
Testo completoAbstract (sommario):
ITC/USA 2005 Conference Proceedings / The Forty-First Annual International Telemetering Conference and Technical Exhibition / October 24-27, 2005 / Riviera Hotel & Convention Center, Las Vegas, Nevada<br>Pulse Code Modulation (PCM) Encoders used in Telemetry Instrumentation systems have traditionally been implemented using sequencer or state-machine based micro-architectures with distributed control and signal acquisition components. This architecture requires the use of many discrete electronic components and custom micro-code programming or state machine development for the control of the systems. The advent of relatively high-speed microcontrollers with embedded signal acquisition subsystems has brought about the ability to implement highly integrated PCM Encoder systems using fewer components and standardized programming methods. This paper will discuss sequencer based PCM encoders for background and then introduce the concept of Microcontroller Based PCM Encoders for Telemetry Instrumentation. Specific design examples will be introduced. Advantages and disadvantages of the two techniques will be discussed.
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Carrier, Grégory. "Bases moléculaires de la variation clonale chez la vigne (Vitis vinifera L.) : approche pangénomique." Thesis, Montpellier, SupAgro, 2011. http://www.theses.fr/2011NSAM0039/document.
Testo completoAbstract (sommario):
L'exploitation de la variation clonale est une des voies d'amélioration utilisée chez un grand nombre de plantes d'intérêts agronomiques telles que la pomme de terre, le café et la vigne. En effet, après plusieurs cycles de reproduction végétative, des caractéristiques agronomiques stables apparaissent donnant naissance à une diversité phénotypique remarquable, appelée « diversité clonale ». Chez la vigne, cette diversité clonale est d'une importance majeure pour les viticulteurs puisqu'elle permet une amélioration variétale sans changer d'identité de cépage en conformité avec la réglementation fixée par Appellations d'Origine Protégée. L'hypothèse la plus parcimonieuse expliquant cette diversité phénotypique clonale est l'accumulation de mutations somatiques au cours des cycles de reproduction végétative. L'objectif de cette thèse a été de dresser un panorama le plus exhaustif possible des différents polymorphismes moléculaires entre les génomes de plusieurs clones. Dans un premier temps trois clones de Pinot ont été séquencés par la technique 454 GS-FLX puis dans un second temps 11 clones de quatre cépages ont été séquencés la technique Illumina HiSeq 2000. Afin d'analyser la grande quantité de données obtenues, nous avons construit un pipeline d'analyse (Bacchus pipeline) permettant d'identifier tous les types de polymorphismes moléculaires entre les différents génomes.Nos résultats permettent, pour la première fois un inventaire exhaustif des polymorphismes moléculaires dans un contexte multiplication végétatif. L'ensemble des mutations polymorphes entre deux clones a pu être identifié, SNPs, indels (2,5 SNPs et 11,5 indels par Mb en moyenne) ainsi que des variations d'ordre structural (larges insertions ou délétions) représentant la classe la plus fréquente (129 évènements par Mb entre deux clones en moyenne). Afin d'évaluer le polymorphisme d'insertion généré par ces éléments nous en avons étudié quatre par une approche S-SAP sur plusieurs niveaux de diversité (inter-espèces, inter-cépages, inter-clones et entre plusieurs tissus d'un même individu). L'analyse phylogénétique au niveau des espèces est conforme à celle réalisée avec d'autres types de marqueurs moléculaires (SSR, SNP). Cependant, une forte instabilité de ces insertions a été confirmée entre les clones et entre les tissus d'un même d'individu. L'identification des clones par une méthodologie moléculaire serait d'une grande importance pour la filère. Pour cet objectif, nos résultats indiquent que les mutations de types SNP et petits indels qui sont certes moins fréquentes que les variations structurales mais qui sont plus stables semblent plus pertinentes pour la mise en place d'une méthodologie d'identification des clones<br>Clonal variation is considered as an effective contribution to breeding programs of vegetatively propagated species with major agronomical interest such as banana, potato, coffee and grape. Indeed, after several propagation cycles, stable and heritable phenotypic variations appear giving rise to a phenotypic variation termed “clonal diversity”. This clonal diversity is very important for wine-growers because it allows preserving cultivars identity in the strict respect of Appellation (A.O.P) wines specifications The most parsimonious hypothesis explaining clonal phenotypic diversity is the accumulation of somatic mutations. The objective of my thesis was to provide a broad description of molecular polymorphisms in the context of vegetative propagation. Three clones were first sequenced by 454 GS-FLX technology and eleven clones were then sequenced with Illumina Hiseq2000 technique. To analyse the high quantity of data obtained, we built a pipeline (Bacchus pipeline) allowing the identification of all existing molecular polymorphisms between different genomes.All polymorphism types were observed: indels and SNPs which have a low polymorphism frequency (2.5 SNPs and 11.5 indels per Mb between two clones in average) and structural variations (large insertions or deletions) which have a high polymorphism frequency (129 per Mb between two clones in average) but are unstable. To evaluate stability and polymorphism level of these transposable elements, we have studied 4 elements using S-SAP method at different diversity levels (inter-species, inter-cultivars, inter-clones and between organs/tissues of a single individual). Our interspecific phylogenetic analysis is similar to other phylogenies performed with SSR or SNPs markers. However, we confirm the high instability of these elements between clones and between tissues in single individuals.Clone identification through molecular methods would be of high significance for the wine industry. SNP or small indels mutations are less frequent but more stable than structural variation and could be used for accurate clone identification
14
Cai, Zheng. "Repetitive sequence analysis for soybean genome sequences." Diss., Columbia, Mo. : University of Missouri-Columbia, 2005. http://hdl.handle.net/10355/4249.
Testo completoAbstract (sommario):
Thesis (M.S.)--University of Missouri-Columbia, 2005.<br>"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.
15
Göran, Sandström. "Procedural Sequencing : a New Form of Procedural Music Creation." Thesis, Högskolan Kristianstad, Sektionen för hälsa och samhälle, 2013. http://urn.kb.se/resolve?urn=urn:nbn:se:hkr:diva-10699.
Testo completoAbstract (sommario):
With increased availability of smartphones, game consoles and computers with capabilities of synthesizing procedural music in real time comes the challenge of realizing new tools for generative music composition for games, inter-media art and musical live performance.This work defines a new method of creating music, “procedural sequencing”, and it presents a musical software that attempts to solve some of the design challenges of bridging interactive elements and more traditional tools for music composition. The software combines aspects of live coding with tracker sequencing.
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Ireland, Ian D. "High sensitivity protein sequencing using fluorescein isothiocyanate for derivatization on a miniaturized sequencer using capillary electrophoresis with laser induced fluorescence detection for product identification." Thesis, National Library of Canada = Bibliothèque nationale du Canada, 2000. http://www.collectionscanada.ca/obj/s4/f2/dsk1/tape2/PQDD_0009/NQ59975.pdf.
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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.
Testo completoAbstract (sommario):
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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Arner, Erik. "Solving repeat problems in shotgun sequencing /." Stockholm, 2006. http://diss.kib.ki.se/2006/91-7140-996-3/.
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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/.
Testo completoAbstract (sommario):
Thesis (M.S.) -- Worcester Polytechnic Institute.<br>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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Dvořák, Pavel. "Sekvencer pro obsluhu krátkovlnné radiostanice." Master's thesis, Vysoké učení technické v Brně. Fakulta elektrotechniky a komunikačních technologií, 2012. http://www.nusl.cz/ntk/nusl-219884.
Testo completoAbstract (sommario):
In this paper we will deal involving short-wave radio station and its control by the sequencer. Mostly it will be a time delay of the PA and the antenna switching relay in the transmitter (TX) to receiver (RX) side. Time delays will be controlled programmatically using ATmega 16 microprocessor, which will form part of the main control sequencer. The delay will set the total time of keying in messages, when we take into account the loss due to delayed first symbol. Keying will be done from several sources, among the main sources will be ordered from keying the radio, telegraph keys, and PC. The transmission signal is used amplitude modulation (SSB) in the CB zone.
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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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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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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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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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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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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.
Testo completoAbstract (sommario):
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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Liakhovitch, Evgueni. "Genetic algorithm using restricted sequence alignments." Ohio : Ohio University, 2000. http://www.ohiolink.edu/etd/view.cgi?ohiou1172598174.
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Philippe, Nicolas. "Développement de méthodes et d'algorithmes pour la caractérisation et l'annotation des transcriptomes avec les séquenceurs haut débit." Phd thesis, Université Montpellier II - Sciences et Techniques du Languedoc, 2011. http://tel.archives-ouvertes.fr/tel-00842810.
Testo completoAbstract (sommario):
Depuis leur apparition, les séquenceurs haut débit ont révolutionné l'étude des transcriptomes à l'échelle du génome. En effet, ils offrent la possibilité de générer des millions, voire des milliards de séquences, appelées reads. Des nouvelles approches transcriptomiques, telles que la Digital Gene Expression (DGE) et le RNA-Sequencing (RNA-Seq), permettent aujourd'hui de répertorier, de quantifier, voire reconstruire tous les transcrits d'une cellule, même les plus rares. Parmi ce type de transcrits se trouvent des ARN non-codants régulateurs ; des variants d'épissages créateurs de protéines ; et aussi des chimères (par fusion de gènes ou trans-épissage). La caractérisation de l'ensemble de ces transcrits représente un réel défi algorithmique, mais suscite aussi un défi biologique car certains peuvent être impliqués dans de nombreux processus cellulaires physiologiques et pathologiques et sont fréquemment décrits dans les cancers.Dans ce travail, nous proposons des algorithmes et des méthodes pour la caractérisation et l'annotation des transcriptomes. Tout d'abord, nous proposons une étude statistique sur la DGE afin d'évaluer l'impact des erreurs de séquences lors de l'analyse des reads. À partir de cette analyse, nous avons développé un pipeline d'annotation pour la DGE. Par le biais de ce premier travail, nous avons pu démontrer que de nombreuses informations étaient partagées entre les reads. Cela nous a amené à concevoir la structure d'indexation Gk arrays qui permet d'organiser une quantité massive de reads de façon à pouvoir interroger rapidement la structure sous forme de requêtes. Enfin, en s'appuyant sur les Gk arrays, nous avons développé CRAC qui est un logiciel spécialisé dans le traitement du RNA-Seq. En intégrant sa propre phase de mapping, CRAC est capable de distinguer les phénomènes biologiques des erreurs de séquences. Ilpermet notamment l'identification de chimères qui sont souvent très faiblement exprimées dans un transcriptome et sont par nature complexe à détecter avec des parties localisées à différents endroits sur le génome.
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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.
Testo completoAbstract (sommario):
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 AlexSys<br>The 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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Wallis, Anne Elizabeth. "Identification of Leishmania genes encoding proteins containing tandemly repeating peptides." Thesis, University of British Columbia, 1987. http://hdl.handle.net/2429/29447.
Testo completoAbstract (sommario):
In order to identify Leishmania proteins which may be immunologically relevant or may play a role in interactions between Leishmania and its mammalian host, a Leishmania major genomic DNA library was constructed in the vector λgt11 and screened with antibodies raised to Leishmania major promastigote membranes. Two recombinant DNA clones were identified which encoded repetitive sequences (Clone 20 and Clone 39). Clone 20 encoded a repetitive peptide of 14 amino acids and clone 39 encoded an unrelated repetitive peptide of 10 amino acids. Analysis of one of these clones, Clone 20, indicated that there were two RNA transcripts of 9500 and 5200 nucleotides expressed which corresponded to this clone in Leishmania major and Leishmania donovani and this expression was not stage-specific. The results of genomic DNA analysis and isolation of additional clones encoding Clone 20 sequences indicated that there were two genes which corresponded to Clone 20 in both Leishmania major and Leishmania donovani and that these genes differed from one another with respect to the number of repeats which they contained. Antibodies against the fusion protein produced by Clone 20 recognized a series of Leishmania major proteins of apparent mol wt 250,000. Analysis of Clone 39 indicated that there was a single transcript of 7500 nucleotides expressed which corresponded to this clone in both Leishmania major and Leishmania donovani and that there was a single gene (or two identical genes) which encoded this transcript.
The genomes of many protozoan parasites exhibit a high degree of plasticity with respect to chromosome size and number. The presence of highly repetitive regions within their DNA may be involved in maintaining this plasticity, allowing the parasite to evolve rapidly under selective pressure. Repetitive regions have been identified within many Plasmodia antigens and have been implicated in the ability of this parasite to evade the host immune system. The presence of Leishmania genes encoding proteins containing tandemly repeating peptides may indicate that these proteins play a similar role in evading the host immune system during the course of Leishmania infections. The possible evolution and functions of repetitive proteins in protozoan parasites is discussed.<br>Medicine, Faculty of<br>Medical Genetics, Department of<br>Graduate
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Lee, Hong-seng Daniel, and 李康善. "Foldback DNA: nucleotide sequence and characterization of MboII repeated sequences in human long foldbackDNA by molecular cloning and hybridization." Thesis, The University of Hong Kong (Pokfulam, Hong Kong), 1987. http://hub.hku.hk/bib/B31231251.
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Dalmaso, Ricardo Curvello. "Identificação e caracterização de grupos de indivíduos segundo padrões de seqüências de atividades multidimensionais." Universidade de São Paulo, 2009. http://www.teses.usp.br/teses/disponiveis/3/3138/tde-21072009-144859/.
Testo completoAbstract (sommario):
O presente estudo procura identificar grupos homogêneos de indivíduos quanto aos padrões de seqüências de atividades diárias que estes realizam. As atividades são caracterizadas por múltiplos atributos, fazendo com que as seqüências sejam multidimensionais. Como atributos, ou características, são considerados a natureza da atividade realizada, ou motivo da viagem, e o período de realização da mesma, ambos separados em categorias. É estudado o efeito da inclusão da forma de acesso à atividade, ou modo de viagem, como uma terceira dimensão. Este atributo, entretanto, dados os resultados obtidos, não é utilizado nas análises finais. É também considerada a adoção de diferentes categorizações para a dimensão motivo. São usados dados da pesquisa Origem e Destino realizada em 1997, na Região Metropolitana de São Paulo. No trabalho são considerados os indivíduos com 12 anos ou mais, com pelo menos duas viagens diárias e com seqüência de viagens iniciada e terminada em sua residência, sem inconsistências internas. O número de indivíduos que atende a estes critérios é 49.616. A classificação, ou agrupamento, das seqüências de atividades em classes ou grupos é feita considerando uma medida de distância ou dissimilaridade calculada entre as seqüências, que é baseada no esforço necessário para igualá-las. Esta medida é chamada de OT-MDSAM (uni-dimensional Optimum Trajectories-based MultiDimensional Sequence Alignment Method). A partir da matriz de dissimilaridades é executado um processo estatístico de agrupamento hierárquico aglomerativo usando o Método de Ward. Os grupos de seqüências formados são analisados considerando características das próprias seqüências e atributos sóciodemográficas e econômicas dos indivíduos que os compõem, e usados em um modelo de segmentação do tipo árvore de decisão, usando o CHAID (Chi-square Automatic Interaction Detector). Resultados indicam que os grupos formados são bastante homogêneos quanto aos padrões de seqüências de atividades que representam e aos indivíduos associados a eles.<br>The main objective of the dissertation is to identify homogeneous groups of individuals, with regard to the daily activity/travel sequences performed in a weekday. Activities are characterized by multiple attributes, thus generating mutidimensional seguences. In this study, the nature of the activity (travel purpose) and the starting period of engagement in the activity (ending time of a trip) were the dimensions considered in the characterization of activities. Access mode to the activity was also considered as a third dimension, but the results had led to the decision not to include it in the final analysis. Alternative categorizations of the activity nature dimension were also studied, that resulted in further disaggregation than adopted in previous analyses of the same data. The study used data from the 1997 Origin-Destination household survey of the Sao Paulo Metropolitan Area. The analysis considered all individuals aged 12 or over that conducted two or more trips (starting and ending at home) on the survey day, resulting in a sample of 49,616 individuals. A sequence alignment method - OT-MDSUM (uni-dimensional Optimum Trajectories-based MultiDimensional Sequence Alignment Method) - was used to compare and calculate distances between pairs of different activity/travel sequences. These distances were then fed into a Ward hierarchical clustering algorithm to create classes of groups of activity/travel patterns. These groups were then analyzed according to the characteristics of the activity/travel sequences included and to the sociodemographic and economic characteristics of individuals who performed these patterns. The data were then utilized to develop a decision tree model using CHAID - Chi-Squared Automatic Interaction Detector, having the group of activity/travel sequences as the response variable and the characteristics of individuals and their families as independent variables. The results indicate that the groups formed through this procedure present a good degree of homogeneity regarding the activity patterns they represent and that they can be clearly associated to the characteristics of the individuals which perform these patterns.
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Yu, Ning. "A Computational Tool for the Prediction of Small Non-coding RNAs in Genome Sequences." OpenSIUC, 2009. https://opensiuc.lib.siu.edu/theses/79.
Testo completoAbstract (sommario):
The purpose of researching bacterial gene expression is to control and prevent the diseases which are caused by bacteria. Recently researchers discovered small non-coding RNAs (ncRNA / sRNA) perform a variety of critical regulatory functions in bacteria. The genome-wide searching for sRNAs, especially the computational method, has become an effective way to predict the small non-coding RNAs because sRNAs have the consistent sequence characteristics. This article proposes a hybrid computational approach, HybridRNA, for the prediction of small non-coding RNAs, which integrates three critical techniques, including secondary structural algorithm, thermo-dynamic stability analysis and sequence conservation prediction. Relying on these computational techniques, our approach was used to search for sRNAs in Streptococcus pyogenes which is one of the most important bacteria for human health. This search led five strongest candidates of sRNA to be predicted as the key components of known regulatory pathways in S. pyogens.
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Local, Andrea. "Cloning of Carbonic Anhydrase from Cotton (Gossypium hirsutum L.)." Thesis, University of North Texas, 1998. https://digital.library.unt.edu/ark:/67531/metadc279044/.
Testo completoAbstract (sommario):
Carbonic anhydrase is a ubiquitous zinc-metalloenzyme that catalyzes the interconversion of carbon dioxide and carbonate and has been found to play a wide range of roles in animals, plants and bacteria. Cotton genomic and cDNA libraries were screened for the plastidial isoform of carbonic anhydrase. The nucleotide sequences of two 1.2 Kb partial cDNA clones were determined. These clones exhibit high homology to carbonic anhydrases from other dicot plants and possess all the expected peptide motifs. For example, serine and threonine rich chloroplastic targeting peptide and conserved zinc binding residues are both present. These clones were utilized to isolate two carbonic anhydrase genes that were shown to encode different isoforms by PCR and RFLP analysis.
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Almeida, André Atanasio Maranhão 1981. "Novas abordagens para o problema do alinhamento múltiplo de sequências." [s.n.], 2013. http://repositorio.unicamp.br/jspui/handle/REPOSIP/275646.
Testo completoAbstract (sommario):
Orientador: Zanoni Dias<br>Tese (doutorado) - Universidade Estadual de Campinas, Instituto de Computação<br>Made available in DSpace on 2018-08-22T15:29:14Z (GMT). No. of bitstreams: 1
Almeida_AndreAtanasioMaranhao_D.pdf: 2248939 bytes, checksum: b57ed5328b80a2fc7f36d1509558e756 (MD5)
Previous issue date: 2013<br>Resumo: Alinhamento de seqüências é, reconhecidamente, uma das tarefas de maior importância em bioinformática. Tal importância origina-se no fato de ser uma operação básica utilizada por diversos outros procedimentos na área, como busca em bases de dados, visualização do efeito da evolução em uma família de proteínas, construção de árvores filogenéticas e identificação de motifs preservados. Seqüências podem ser alinhadas aos pares, problema para o qual já se conhece algoritmo exato com complexidade de tempo O(l2), para seqüências de comprimento l. Pode-se também alinhar simultaneamente três ou mais seqüências, o que é chamado de alinhamento múltiplo de seqüências (MSA, do inglês Multiple Sequence Alignment ). Este, que é empregado em tarefas como detecção de padrões para caracterizar famílias protéicas e predição de estruturas secundárias e terciárias de proteínas, é um problema NP - Difícil. Neste trabalho foram desenvolvidos métodos heurísticos para alinhamento múltiplo de seqüências de proteína. Estudaram-se as principais abordagens e métodos existentes e foi realizada uma série de implementações e avaliações. Em um primeiro momento foram construídos 342 alinhadores múltiplos utilizando a abordagem progressiva. Esta, que é uma abordagem largamente utilizada para construção de MSAs, consiste em três etapas. Na primeira delas é computada a matriz de distâncias. Em seguida, uma árvore guia é gerada com base na matriz e, finalmente, o MSA é construído através de alinhamentos de pares, cuja ordem é definida pela árvore. Os alinhadores desenvolvidos combinam diferentes métodos aplicados a cada uma das etapas. Para a computação das matrizes de distâncias foram desenvolvidos dois métodos, que são capazes também de gerar alinhamentos de pares de seqüências. Um deles constrói o alinhamento com base em alinhamentos locais e o outro utiliza uma função logarítmica para a penalização de gaps. Foram utilizados ainda outros métodos disponíveis numa ferramenta chamada PHYLIP. Para a geração das árvores guias, foram utilizados os métodos clássicos UPGMA e Neighbor Joining. Usaram-se implementações disponíveis em uma ferramenta chamada R. Já para a construção do alinhamento múltiplo, foram implementados os métodos seleção por bloco único e seleção do par mais próximo. Estes, que se destinam a seleção xiii do par de alinhamentos a agrupar no ciclo corrente, são comumente utilizados para tal tarefa. Já para o agrupamento de um par de alinhamentos, foram implementados 12 métodos inspirados em métodos comumente utilizados - alinhamento de consensos e alinhamento de perfis. Foram feitas todas as combinações possíveis entre esses métodos, resultando em 342 alinhadores. Eles foram avaliados quanto à qualidade dos alinhamentos que geram e avaliou-se também o desempenho dos métodos, utilizados em cada etapa. Em seguida foram realizadas avaliações no contexto de alinhamento baseado em consistência. Nesta abordagem, considera-se MSA ótimo aquele que estão de acordo com a maioria dos alinhamentos ótimos para os n(n ? 1)/2 alinhamentos de pares contidos no MSA. Alterações foram realizadas em um alinhador múltiplo conhecido, MUMMALS, que usa a abordagem. As modificações foram feitas no método de contagem k-mer, assim como, em outro momento, substituiu-se a parte inicial do algoritmo. Foram alterados os métodos para computação da matriz de distâncias e para geração da árvore guia por outros que foram bem avaliados nos testes realizados para a abordagem progressiva. No total, foram implementadas e avaliadas 89 variações do algoritmo original do MUMMALS e, apesar do MUMMALS já produzir alinhamentos de alta qualidade, melhoras significativas foram alcançadas. O trabalho foi concluído com a implementação e a avaliação de algoritmos iterativos. Estes se caracterizam pela dependência de outros alinhadores para a produção de alinhamentos iniciais. Ao alinhador iterativo cabe a tarefa de refinar tais alinhamentos através de uma série de ciclos até que haja uma estabilização na qualidade dos alinhamentos. Foram implementados e avaliados dois alinhadores iterativos não estocásticos, assim como um algoritmo genético (GA) voltado para a geração de MSAs. Nesse algoritmo genético, implementado na forma de um ambiente parametrizável para execução de algoritmos genéticos para MSA, chamado ALGAe, foram realizadas diversas experiências que progressivamente elevaram a qualidade dos alinhamentos gerados. No ALGAe foram incluídas outras abordagens para construção de alinhamentos múltiplos, tais como baseada em blocos, em consenso e em modelos. A primeira foi aplicada na geração de indivíduos para a população inicial. Foram implementados alinhadores baseados em blocos usando duas abordagens distintas e, para uma delas, foram implementadas cinco variações. A segunda foi aplicada na definição de um operador de cruzamento, que faz uso da ferramenta M-COFFEE para realizar alinhamentos baseados em consenso a partir de indivíduos da população corrente do GA, e a terceira foi utilizada para definir uma função de aptidão, que utiliza a ferramenta PSIPRED para predição das estruturas secundárias das seqüências. O ALGAe permite a realização de uma grande variedade de novas avaliações<br>Abstract: Sequence alignment is one the most important tasks of bioinformatics. It is a basic operation used for several procedures in that domain, such as sequence database searches, evolution effect visualization in an entire protein family, phylogenetic trees construction and preserved motifs identification. Sequences can be aligned in pairs and generate a pairwise alignment. Three or more sequences can also be simultaneously aligned and generate a multiple sequence alignment (MSA). MSAs could be used for pattern recognition for protein family characterization and secondary and tertiary protein structure prediction. Let l be the sequence length. The pairwise alignment takes time O(l2) to build an exact alignment. However, multiple sequence alignment is a NP-Hard problem. In this work, heuristic methods were developed for multiple protein sequence alignment. The main approaches and methods applied to the problem were studied and a series of aligners developed and evaluated. In a first moment 342 multiple aligners using the progressive approach were built. That is a largely used approach for MSA construction and is composed by three steps. In the first one a distance matrix is computed. Then, a guide tree is built based on the matrix and finally the MSA is constructed through pairwise alignments. The order to the pairwise alignments is defined by the tree. The developed aligners combine distinct methods applied to each of steps. Then, evaluations in the consistency based alignment context were performed. In that approach, a MSA is optimal when agree with the majority along all possible optimal pairwise alignments. MUMMALS is a known consistency based aligner. It was changed in this evaluation. The k-mer counting method was modified in two distinct ways. The k value and the compressed alphabet were ranged. In another evaluation, the k-mer counting method and guide tree construction method were replaced. In the last stage of the work, iterative algorithms were developed and evaluated. Those methods are characterized by other aligner's dependence. The other aligners generate an initial population and the iterative aligner performs a refinement procedure, which iteratively changes the alignments until the alignments quality are stabilized. Several evaluations were performed. However, a genetic algorithm for MSA construction stood out along this stage. In that aligner were added other approaches for multiple sequence alignment construction, such as block based, consensus based and template based. The first one was applied to initial population generation, the second one was used for a crossover operator creation and the third one defined a fitness function<br>Doutorado<br>Ciência da Computação<br>Doutor em Ciência da Computação
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Lee, Hong-seng Daniel. "Foldback DNA : nucleotide sequence and characterization of MboII repeated sequences in human long foldback DNA by molecular cloning and hybridization /." [Hong Kong : University of Hong Kong], 1987. http://sunzi.lib.hku.hk/hkuto/record.jsp?B12263643.
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Müller, Rodrigo Temp. "DESCRIÇÃO E POSICIONAMENTO FILOGENÉTICO DE UM NOVO ESPÉCIME DE SAUROPODOMORFA DA FORMAÇÃO CATURRITA." Universidade Federal de Santa Maria, 2016. http://repositorio.ufsm.br/handle/1/5332.
Testo completoAbstract (sommario):
Coordenação de Aperfeiçoamento de Pessoal de Nível Superior<br>The present dissertation aims to present the osteological anatomy of an early sauropodomorph found in Triassic rocks from the municipality of Agudo, Rio Grande do Sul (RS), Brazil. In addition, it aims to tests the biostratigraphic utility of this specimen. CAPPA/UFSM 0002 is composed of postcranial elements from the locality called Sítio Wachholz, ascribed to the Caturrita Formation. Some typical features present in prosauropods are verified in the specimen. For instance, the concave caudal margin of the neural spines of the medial trunk vertebrae, the convex proximal surface of the metacarpal V, and the distal end of the ischium higher than two times the width. On the other hand, typical features of more derived groups than Plateosauridae are absent and the slender shape of the first phalanx of the digit I of the foot corresponds to a common state of basalmost sauropodomorphs. A comparative and phylogenetic analysis among several early sauropodomorphs suggests affinities with Unaysaurus tolentinoi, the only unequivocal sauropodomorph from Caturrita Formation. Based upon such results, a biostratigraphic framework is proposed, which includes the Wachholz, Botucaraí Hill (Candelária, RS), and the Água Negra sites (São Martinho da Serra, RS), this last one so far producing the only record of U. tolentinoi. This corresponds to the first biostratigraphic framework proposed based on fossil vertebrates for the type locality of U. tolentinoi. Considering the presence of the genus Jachaleira in the Los Colorados Formation (Argentina) and in the Botucaraí Hill Site, an early Norian age is suggested to the correlated sites, as recent studies point this age to the portion that yielded Jachaleria in the Los Colorados Formation. Such age places U. tolentinoi and the other sauropodomorphs evaluated here in a unique position regarding the evolutionary history of the sauropodomorphs, suggesting that they lived in a transitional moment, between a period of low representativeness to an of extreme abundance of the group on Earth.<br>A presente dissertação tem como objetivo principal apresentar a anatomia óssea de um sauropodomorfo primitivo descoberto em rochas Triássicos no município de Agudo, Rio Grande do Sul (RS), Brasil. Além disso, objetiva-se testar o espécime em estudos de correlação bioestratigráfica. O espécime CAPPA/UFSM 0002 é composto por elementos pós-cranianos recuperados na localidade conhecida como Sítio Wachholz, atribuída à Formação Caturrita. É possível verificar a presença de características consideradas típicas dos prossaurópodes . Por exemplo, a forma côncava da margem caudal dos processos espinhosos das vértebras mediais truncais, a superfície convexa da extremidade proximal do metacarpal V e a extremidade distal do ísquio com altura maior do que duas vezes sua largura. Por outro lado, feições típicas de grupos mais derivados do que Plateosauridae não foram encontradas e a primeira falange do digito I do pé apresenta morfologia delgada, comum em sauropodomorfos mais basais. Uma análise comparativa e filogenética dentre diversos sauropodomorfos primitivos sugere afinidades com Unaysaurus tolentinoi, até o momento o único sauropodomorfo inequivoco da Formação Caturrita. Com base em tais resultados, é proposto um esquema de correlação entre os sítios Wachholz, Botucaraí (Candelária, RS) e Água Negra (São Martinho da Serra, RS), este último tendo produzido o único registro de U. tolentinoi até o momento. Assim, esta é a primeira proposta bioestratigrafica envolvendo a localidade tipo de U. tolentinoi com base em vertebrados fósseis. Dada a presença do gênero Jachaleria na Formação Los Colorados (Argentina) e no Sítio Cerro Botucaraí, é sugerida idade Noriana inicial para os sítios correlacionados neste esquema, uma vez que estudos recentes apontam a mesma idade para a porção com registro do gênero na Formação Los Colorados. Esta idade coloca U.tolentinoi e os outros espécimes avaliados aqui em uma posição única na historia evolutiva dos sauropodomorfos, sugerindo que eles viveram em um momento de transição de um período de baixa representatividade para um de extrema abundância do grupo na Terra.
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Mallmann, Rafael Mendes. "Arquiteturas em hardware para o alinhamento local de sequências biológicas." reponame:Biblioteca Digital de Teses e Dissertações da UFRGS, 2010. http://hdl.handle.net/10183/56841.
Testo completoAbstract (sommario):
Bancos de dados biológicos utilizados para comparação e alinhamento local de sequências tem crescido de forma exponencial. Isso popularizou programas que realizam buscas nesses bancos. As implementações dos algoritmos de alinhamento de sequências Smith- Waterman e distância Levenshtein demonstraram ser computacionalmente intensivas e, portanto, propícias para aceleração em hardware. Este trabalho descreve arquiteturas em hardware dedicado prototipadas para FPGA e ASIC para acelerar os algoritmos Smith- Waterman e distância Levenshtein mantendo os mesmos resultados obtidos por softwares. Descrevemos uma nova e eficiente unidade de processamento para o cálculo do Smith- Waterman utilizando affine gap. Também projetamos uma arquitetura que permite particionar as sequências de entrada para a distância Levenshtein em um array sistólico de tamanho fixo. Nossa implementação em FPGA para o Smith-Waterman acelera de 275 a 494 vezes o algoritmo em relação a um computador com processador de propósito geral. Ainda é 52 a 113% mais rápida em relação, segundo nosso conhecimento, as mais rápidas arquiteturas recentemente publicadas.<br>Bioinformatics databases used for sequence comparison and local sequence alignment are growing exponentially. This has popularized programs that carry out database searches. Current implementations of sequence alignment methods based on Smith- Waterman and Levenshtein distance have proven to be computationally intensive and, hence, amenable for hardware acceleration. This Msc. Thesis describes an FPGA and ASIC based hardware implementation designed to accelerate the Smith-Waterman and Levenshtein distance maintaining the same results yielded by general softwares. We describe an new efficient Smith-Waterman affine gap process element and a new architecture to partitioning and maping the Levenshtein distance into fixed size systolic arrays. Our FPGA Smith-Waterman implementation delivers 275 to 494-fold speed-up over a standard desktop computer and is also about 52 to 113% faster, to the best of our knowledge, than the fastest implementation in a most recent family of accelerators.
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Dew, Patrick. "SEQUENCE." Kent State University / OhioLINK, 2008. http://rave.ohiolink.edu/etdc/view?acc_num=kent1208712717.
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Kwasigroch, Jean-Marc. "Etude de faibles identites de sequences dans les proteines globulaires : proposition d'une taxonomie des boucles et etablissement d'une relation entre sequence et structure." Paris 6, 1996. http://www.theses.fr/1996PA066218.
Testo completoAbstract (sommario):
Une banque de boucles de trois a huit acides amines de long a ete constituee. D'une analyse statistique des conformations, il ressort que les boucles sont constituees de deux parties: les residus extremes, en contact avec les structures secondaires que la boucle relie, et l'interieur. Les conformations des residus de bord sont correlees a la nature de la structure secondaire voisine. Par contre, les residus centraux adoptent des conformations non correlees d'un residu au suivant. Le fort pourcentage de conformations a#l, principalement dues aux glycines et decroissant avec la taille de la boucle, est necessaire pour induire la flexibilite qui permet aux boucles de remplir les contraintes geometriques de fermeture au niveau des flancs. Un algorithme d'agregation a permis de regrouper dans une meme famille les boucles de meme longueur presentant des similarites structurales. Dans chaque famille structurale, une signature en sequence et en conformation a ete deduite des que la frequence d'apparition d'un residu ou d'une conformation en une position est plus grande que celle due a une distribution equirepartie sur l'ensemble des familles a la meme position. Il s'agit ainsi de faire apparaitre des residus et des conformations typiques d'une famille et de relier sequence et structure dans les boucles. Une classification des familles est proposee qui repose sur deux parametres geometriques moyens a l'interieur de chaque famille. Celle-ci permet a la fois de separer les differentes longueurs de boucles, mais aussi les differentes familles d'une longueur donnee. Quelques applications de cette caracterisation sont proposees, qu'il s'agisse de l'etude des tripeptides comme marqueurs specifiques des boucles, la detection des structures secondaires, ou l'utilisation en modelisation moleculaire pour choisir la meilleure boucle en etant capable d'affecter a une boucle sa famille structurale avec comme seule information la sequence de la boucle
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Agrawal, Ankit. "Sequence-specific sequence comparison using pairwise statistical significance." [Ames, Iowa : Iowa State University], 2009.
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Leonchiks, Ainars. "Regulation of protein degradation by virus derived repeated amino acid sequences /." Stockholm, 2002. http://diss.kib.ki.se/2002/91-7349-206-x/.
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Gregio, Bruno Chioderoli [UNESP]. "Sequências de números reais e as famosas constantes matemáticas e, π e ϕ". Universidade Estadual Paulista (UNESP), 2017. http://hdl.handle.net/11449/150789.
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Previous issue date: 2017-04-28<br>Este trabalho apresenta uma proposta para o estudo de sequências de números reais, sobretudo no ensino médio. A partir da definição de uma sequência, estudamos os casos particulares das progressões aritméticas e geométricas. Como sabemos, é praxe os livros didáticos encerrarem o assunto sobre sequências por aqui, porém neste trabalho avançamos os estudos apresentando a noção de limite de uma sequência e os principais resultados sobre sequências convergentes. Tendo compreendido que cada número real pode ser obtido como o limite de uma sequência de Cauchy de números racionais, apresentamos as famosas constantes matemáticas e, π e φ, além dos números da forma √ a, como o limite de certas sequências de Cauchy de números racionais.<br>This work presents a proposal for the study on sequences of real numbers, especially in high school. From the de nition of a sequence, we study the particular cases of arithmetic and geometric progressions. As we know, it is usual for textbooks to terminate the subject of sequences here, but in this work we have advanced the studies presenting the notion of limit of a sequence and the main results on convergent sequences. Having understood that each real number can be obtained as the limit of a Cauchy sequence of rational numbers, we introduce the famous mathematical constants e, π and ϕ, beyond the numbers of the form √a, as the limit of certain Cauchy sequences of rational numbers.
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Chia, Nicholas Lee-Ping. "Sequence alignment." Columbus, Ohio : Ohio State University, 2006. http://rave.ohiolink.edu/etdc/view?acc%5Fnum=osu1154616122.
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Matthews, Trevor W. "In Sequence." Bowling Green State University / OhioLINK, 2012. http://rave.ohiolink.edu/etdc/view?acc_num=bgsu1332165226.
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Garbett, Gary. "Insequential Sequence." VCU Scholars Compass, 2010. http://scholarscompass.vcu.edu/etd/2277.
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Since childhood, my passion to create has driven me to search for the simplest truths within the world I live in. Throwbacks of pop culture have always decorated my life and their influences are directly reflected in my work. The nightly news, advertisements, pulp magazines, film, and music all play an extremely important role in my work as each influence becomes a layer of spirit and emotion in my mixed media paintings and photography. It’s those ordinary and mundane gifts that I find in each normal day that spill the truth and the essence of my life into my art. Popular culture has always filled my life with vivacity, passion, and a yearning for creativity. Admittedly, I’ve long been an artist that gets lost in the contemporary message of my work. I do after all own it and somewhere in my creative mind the process of creation and the object as art become my unified gospel in a sacred delivery and message. I absorb my surroundings, dissect it, rearrange it, and spit it back out to the world as a reinterpretation of the original, and on occasion transform it into something totally original within itself.
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Coccia, Marco Anthony. "Identification and cloning of amplified DNA sequences by a modified-in-gel renaturation technique: Isolation of an amplified DNA sequence from a human sarcoma." Diss., The University of Arizona, 1991. http://hdl.handle.net/10150/185368.
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A modified in gel renaturation technique has been developed which detects DNA sequence amplifications of ≥10-fold without prior identification of the target gene. In order to determine the sensitivity of detection and applicability of modified in gel renaturation, primary human tumor cultures and drug resistant human cell lines with identified cellular gene amplifications were assayed. The modified in gel renaturation technique was then used to screen 71 human tumor cell lines and direct tumor biopsies for amplified sequences. Particular emphasis was placed on screening cell lines derived from human melanoma and direct tumor samples from adult sarcomas. Four of 55 cell lines tested had amplification ≥10-fold of previously known cellular oncogenes. None of the 25 melanoma short term cultures tested positive by this assay. One of 16 adult sarcoma samples (a malignant fibrous histiocytoma (MFH)) tested positive for DNA sequence amplification >10-fold. The amplified DNA present in this MFH, (termed ST-23987), was not identified by Southern blot analysis with a panel of oncogene probes previously reported as amplified in other human malignancies. In order to further characterize the amplified DNA in ST-23987, DNA was subjected to in gel renaturation cloning procedures followed by PCR modified cloning. Of 55 clones isolated and analyzed, four cloned inserts (termed pMAC895, pMAC15, pMAC20, and pMAC30) were amplified between 10-to-15-fold in ST-23987DNA. Several other adult sarcomas were probed with these four clones and three other instances of amplification were identified by Southern blot analysis with probes generated from pMAC15 and pMAC30 (found in tumors ST-24609, 870141 and ST-23493). A bacteriophage lambda genomic library was constructed from DNA isolated from a ST-23493. Four clones representing ∼34 kb of the amplified domain (designated 493.1, 493.2, 493.4, and 493.5) were isolated using clones pMAC15 and pMAC30 as probes. Plasmid subclones generated from the EcoRI fragments of the amplified bacteriophage lambda clones (termed p10.5, p6.0, p5.2, p5.0, p4.7, p2.8, and p0.5) were used as probes against Northern blots of sarcoma mRNA in an attempt to identify transcribed sequences within the cloned regions of the amplification unit. The hypothesized target gene carried within the amplification unit will likely be important to the progression, diagnosis and treatment of adult sarcoma, irrespective of the target gene identity.