Global ETD Search
Search theses and dissertations gathered from participating repositories worldwide. Every result links back to the library that holds it. No account is needed.
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Showing 1 to 20 of 38 for “"RNA secondary structure"”.
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RNA secondary structure prediction using hybrid methods
… work presents a novel two-stage framework for RNA secondary structure prediction, introducing deep learning models that address local substructure prediction and global structure assembly. Drawing insights from RNA folding kinetics, the stage-1 (S1) model proposes local substructures as …
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Advanced tools for RNA secondary structure analysis
The analysis of RNA secondary structure has become more and more important throughout the last decades after it was recognised that RNA does not only serve as a passive messenger (mRNA), but also as a functional compound of the cell. Furthermore, it was elucidated that mainly the structure rather …
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Review of algorithms for RNA secondary structure prediction with pseudoknots
Pseudoknots are structures that are formed from the base pairing of an RNA secondary loop structure with a complementary base which lies somewhere outside of the loop. The result is a structure, which plays a vital role in cell structure rigidity, regulation of protein synthesis, and in the …
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RNA secondary structure detection programs with an emphasis on covariance models
RNA secondary structure prediction requires a different approach from traditional alignment methods. Functional RNAs often have their secondary structure better conserved than their primary structure. Covariance models, probabilistic models that utilize stochastic-context-free grammars, are one …
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Thermodynamics of neutral sets and sequence length changes in the genotype-phenotype map of RNA secondary structure
The genotype-phenotype (GP) map of RNA secondary structure connects RNA sequences and the corresponding folded molecular structures. This relationship is required for modelling the evolution of functional RNA structures. In this thesis, we fill two gaps in the understanding of the RNA GP map: we …
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Exploring the phylodynamics, genetic reassortment and RNA secondary structure formation patterns of orthomyxoviruses by comparative sequence analysis
RNA viruses are among the most virulent microorganisms that threaten the health of humans and livestock. Among the most socio-economically important of the known RNA viruses are those found in the family Orthomyxovirus. In this era of rapid low-cost genome sequencing and advancements in …
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Structural Properties of Genotype-Phenotype Maps: Models, Estimates and Evolution
… The second part focuses on the network community structure of NCs in the GP map of RNA secondary structure. In particular, a way to reveal the hierarchical community structure solely from the sequence constraints and composition of the genotypes forming a NC is studied. Further, a way to estimate …
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Development of pattern recognition technique for classification of RNA secondary structures by small molecules
<p>Three-dimensional RNA structures are notoriously difficult to determine, and the link between secondary structure and RNA conformation is only beginning to be understood. In this dissertation, I will discuss the development of a pattern recognition technique which utilizes differential binding …
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Kinetic and mutational studies of two RNA-interacting enzymes
Cellular enzymes interact with RNA substrates at several key stages in an organism's life cycle, particularly during the processes of transcription and translation. A more detailed description of enzyme mechanistic features and kinetic parameters is important both for understanding molecular …
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Unraveling the interactions between MBNL1 protein and its RNA targets
The muscleblind-like protein 1 (MBNL1) is an RNA binding protein with four conserved zinc fingers that plays an important role in the regulation of alterative splicing. It interacts with pre-mRNA and promotes the inclusion or exclusion of exons to form different mRNA transcripts. Besides its …
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Investigation of the Molecular Interaction Between Pyr mRNA and the Bacillus Subtilis Attenuation Regulatory Protein, PyrR
… using progressively shorter variants of BL2 mRNA determined that the minimal RNA necessary for tight PyrR binding was 28 nt long. The stoichiometry of the PyrR-pyr mRNA interaction was determined to be equimolar using a gel mobility shift titration assay. The effects of 31 structural variants …
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A Predictive Model Which Uses Descriptors of RNA Secondary Structures Derived from Graph Theory.
<p>The secondary structures of ribonucleic acid (RNA) have been successfully modeled with graph-theoretic structures. Often, simple graphs are used to represent secondary RNA structures; however, in this research, a multigraph representation of RNA is used, in which vertices represent stems and …
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Identification of evolutionarily conserved nucleic acid secondary structures within viral genomes
… nucleotide sequences such as certain DNA and RNA virus genomes form complex secondary structures through Watson-Crick base-pairing interactions between bases on the same DNA or RNA strand. Both computational and experimental methods are available for determining the secondary structure …
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RNA folding via algebraic dynamic programming
… and solve one of the open problems. Ab initio RNA secondary structure folding of a single sequence was chosen as a perfect fit to the requirements. First, because of the compactness of the field, showing a clear path from the first description of the Nearest Neighbor model by Tinoco and others …
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RNA structure analysis : algorithms and applications
… thesis, efficient algorithms for aligning RNA secondary structures and mining unknown RNA motifs are presented. As the major contribution, a structure alignment algorithm, which combines both primary and secondary structure information, can find the optimal alignment between two given …
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A data science approach to pattern discovery in complex structures with applications in bioinformatics
… for discovering patterns or motifs from complex structures, particularly complex RNA structures. RNA secondary and tertiary structure motifs are very important in biological molecules, which play multiple vital roles in cells. A lot of work has been done on RNA motif annotation. However, pattern …
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Graphs, matrices, and populations : linear algebraic techniques in theoretical computer science and population genetics
… Siberians. Finally, we turn to the problem of RNA secondary structure design. In this problem, we want to find RNA sequences that fold to a given secondary structure. We propose a novel global sampling approach, based on the recently developed RNAmutants algorithm, and show that it has numerous …
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Characterizing Human Transfer RNAs by Hydro-tRNAseq and PAR-CLIP
<p>The participation of tRNAs in fundamental aspects of biology and disease necessitates an accurate, experimentally confirmed annotation of tRNA genes, and curation of precursor and mature tRNA sequences. This has been challenging, mainly because RNA secondary structure and nucleotide …
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Understanding regulation of mRNA by RNA binding proteins
Posttranscriptional regulation of mRNA by RNA-binding proteins plays key roles in regulating the transcriptome over the course of development, between tissues and in disease states. The specific interactions between mRNA and protein are controlled by the proteins' inherent affinities for different …
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RNA : algorithms, evolution and design
… 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 …
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