Browsing by Subject "Comparative analysis"
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Item Distances and proximities : Havana and San Juan from the point of view of literature and oral histories(2015-05) Mercado Diaz, Mario Edgardo; Salgado, César Augusto; Merabet, Sofian, 1972-Cuba y Puerto Rico have for long been considered sister islands, fighting together against the influences of the Spanish Empire and the United States. The decade of the 1950s, however, proved to be the splitting point for both islands, sending them into very different trajectories of development. In their shared experience of Spanish colonization and USA interventions, how do San Juan and Havana residents perceive and use space today in their particular socio-political contexts and how does this affect the resident's sense of citizenship? I closely engage with the different urban spaces using ethnographic data and photographs taken during my recent fieldwork, creative texts describing said spaces and case studies examining the formation of racial, gender and class identities. Focusing on a specific place on the Malecón, Havana's iconic esplanade, I examine how practices of leisure, intimacy (e.g. erotic homosexual and heterosexual encounters), and self-expression challenge the revolutionary rhetoric of "sameness" (i.e. absence of race, class, crime or gender violence). As for San Juan, I dissect the layers of significance in public visual representation, as exemplified in the artwork painted over an abandoned house in Santurce, the site for queer, artistic and marginal expression. The scene, two black women drinking on the porch, rescues a sense of citizenship lost to the class and racial polarization, fragmentation, and the "ruination" of San Juan. Finally, I argue that an archipelagic city, composed of the descriptions of specific places in different cities, has been created in the sea, a space of crossing, endurance and death, within these inter-capillary exchanges of people, cultures and habits. This archipelagic city, not spoken about directly but referenced semantically, aids in the construction of trans-national identities and perspectives, specific perceptions on time and space, and the production of media and cultural forms of expression. My goal is to tie together these narrative strands linking trans-oceanic places into an urban map surpassing its own geographical context.Item Improving secondary structure prediction with covariation analysis and structure-based alignment system of RNA sequences(2013-12) Shang, Lei, active 2013; Gutell, RobinRNA molecules form complex higher-order structures which are essential to perform their biological activities. The accurate prediction of an RNA secondary structure and other higher-order structural constraints will significantly enhance the understanding of RNA molecules and help interpret their functions. Covariation analysis is the predominant computational method to accurately predict the base pairs in the secondary structure of RNAs. I developed a novel and powerful covariation method, Phylogenetic Events Count (PEC) method, to determine the positional covariation. The application of the PEC method onto a bacterial 16S rRNA sequence alignment proves that it is more sensitive and accurate than other mutual information based method in the identification of base-pairs and other structural constraints of the RNA structure. The analysis also discoveries a new type of structural constraint – neighbor effect, between sets of nucleotides that are in proximity in the three dimensional RNA structure with weaker but significant covariation with one another. Utilizing these covariation methods, a proposed secondary structure model of an entire HIV-1 genome RNA is evaluated. The results reveal that vast majority of the predicted base pairs in the proposed HIV-1 secondary structure model do not have covariation, thus lack the support from comparative analysis. Generating the most accurate multiple sequence alignment is fundamental and essential of performing high-quality comparative analysis. The rapid determination of nucleic acid sequences dramatically increases the number of available sequences. Thus developing the accurate and rapid alignment program for these RNA sequences has become a vital and challenging task to decipher the maximum amount of information from the data. A template-based RNA sequence alignment system, CRWAlign-2, is developed to accurately align new sequences to an existing reference sequence alignment based on primary and secondary structural similarity. A comparison of CRWAlign-2 with eight alternative widely-used alignment programs reveals that CRWAlign-2 outperforms other programs in aligning new sequences with higher accuracy. In addition to aligning sequences accurately, CRWAlign-2 also creates secondary structure models for each sequence to be aligned, which provides very useful information for the comparative analysis of RNA sequences and structures. The CRWAlign-2 program also provides opportunities for multiple areas including the identification of chimeric 16S rRNA sequences generated in microbiome sequencing projects.Item Improving the prediction of RNA secondary structure and automatic alignment of RNa sequences(2012-05) Gardner, David Paul; Gutell, Robin; Ren, Pengyu; Browning, Karen; Russell, Rick; Makarov, Dmitrii E.; Miranker, DanielThe accurate prediction of an RNA secondary structure from its sequence will enhance the experimental design and interpretation for the increasing number of scientists that study RNA. While the computer programs that make these predictions have improved, additional improvements are necessary, in particular for larger RNAs. The first major section of this dissertation is concerned with improving the prediction accuracy of RNA secondary structures by generating new energetic parameters and evaluating a new RNA folding model. Statistical potentials for hairpin and internal loops produce significantly higher prediction accuracy when compared with nine other folding programs. While more improvements can be made to the energetic parameters used by secondary structure folding programs, I believe that a new approach is also necessary. I describe a RNA folding model that is predicated on a large body of computational and experimental work. This model includes energetics, contact distance, competition and a folding pathway. Each component of this folding model is evaluated and substantiated for its validity. The statistical potentials were created with comparative analysis. Comparative analysis requires the creation of highly accurate multiple RNA sequence alignments. The second major section of this dissertation is focused on my template-based sequence aligner, CRWAlign. Multiple sequence aligners generally run into problems when the pairwise sequence identity drops too low. By utilizing multiple dimensions of data to establish a profile for each position in a template alignment, CRWAlign is able to align new sequences with high accuracy even for pairs of sequence with low identity.