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 42 for “"sequence comparison"”.
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Aspects of biological sequence comparison
Thesis (Ph. D)--Massachusetts Institute of Technology, Dept. of Mathematics, 1987.
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Sequence comparison and the prediction of protein function
Thesis (Ph. D.)--Massachusetts Institute of Technology, Dept. of Biology, 1986.
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Robust and Efficient Algorithms for Protein 3-D Structure Alignment and Genome Sequence Comparison
Sequence analysis and structure analysis are two of the fundamental areas of bioinformatics research. This dissertation discusses, specifically, protein structure related problems including protein structure alignment and query, and genome sequence related problems including haplotype …
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New algorithms for EST clustering
Summary: Expressed sequence tag database is a rich and fast growing source of data for gene expression analysis and drug discovery. Clustering of raw EST data is a necessary step for further analysis and one of the most challenging problems of modem computational biology. There are a few systems, …
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Implementation of a Neural Network-Based ASIC Chip for Mobile DNA Devices
… and an Edit Distance (ED) accelerator for sequence comparison. The proposed SoC architecture, based on an open-source RISC-V core, features hardware accelerators tailored for the computational demands of nanopore DNA sequencing. Performance evaluation was conducted in two stages: first …
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Mathematical Models, Algorithms, and Statistics of Sequence Alignment
<p>The problem of biological sequence comparison arises naturally in an attempt to explain many biological phenomena. Due to the combinatorial structure and pattern preserving properties of the sequences it attracted not only biologists, but also mathematicians, statisticians and computer …
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Structure and Mechanism of a Eukaryotic FMN Adenylyltransferase
… role in flavocoenzyme homeostasis regulation. By sequence comparison, bacterial and eukaryotic FMNAT enzymes belong to two different protein superfamilies and apparently utilize different set of active site residues to accomplish the same chemistry. Extensive biochemical studies from endogenous …
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Developing computational methods to enhance understanding in glioma progression
… of pre-alignment sequencing data. Alignment-free sequence comparison is a method which has been in development in a wider biological context since the 1970s. However, thus far it has only been used in a phylogentic sense to investigate relationships between organisms. This thesis explores the …
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The primary structures and the evolutionary consequences of the olisthodiscus luteus histone proteins
… luteus diverged from the animal line. By sequence comparison, the most closely related histone sequence to the algae was found to be that of the echinodermata. An endosymbiotic event between an echinodermata ancestor and a primitive unicellular alga is hypothesised in an attempt to explain …
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Estimation and Comparison of HIV-Specific Substitution Matrices
… acid substitution matrices are commonly used for sequence alignment, phylogenetic inference and sequence comparison. Empirical organism-specific substitution matrices constructed using only sequence data from a particular organism are thought to lead to more accurate analyses. In HIV research, the …
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Searching Biological Sequence Databases Using Distributed Adaptive Computing
… common type of processing involves searching a sequence database for the most similar sequences. Here we present a distributed database search system that utilizes adaptive computing technologies. The search is performed using the Smith-Waterman algorithm, a common sequence comparison algorithm. …
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A new approach to feature extraction for RNA structure comparision
In recent years, RNA structural comparison becomes a crucial problem in bioinformatics research. Generally, it is a popular approach for representing the RNA secondary structures with arc-annotation sets. Several methods can be used to compare two RNA structures, such as tree edit distance, longest …
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Determination of the Binding Site and the Key Amino Acids on Maize β-Glucosidase Isozyme Glu1 Involved in Binding to β-Glucosidase Aggregating Factor (BGAF)
… up the BGAF binding site on maize Glu1. However, sequence comparison between sorghum β-glucosidases (dhurrinases, Dhr1 and Dhr2), to which BGAF does not bind, and maize β-glucosidases, and an examination of the 3-D structure of Glu1 suggested that the BGAF binding site on Glu1 is much smaller than …
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X-ray Crystallography of Inositol Dehydrogenase Enzymes
… assigned as myo-inositol dehydrogenases by sequence comparison. The enzyme catalyzes the reversible conversion of myo-inositol to scyllo-inosose and the concurrent reduction of NAD+ to NADH. iolG1 was subsequently determined to be a myo-inositol dehydrogenase but iolG2 was determined to be a …
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Biophysical Characterization Of A Proline Mutant Of Neural Cadherin
… cadherin (ncad and ecad) are very similar in sequence comparison, but differ in kinetics of dimer assembly and dimer affinity in the presence or absence of calcium. The single most obvious difference in the strand swapped interface is a proline in ncad and a glutamate in ecad in position 16. …
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Characterization of mutant N², N²-dimethylguanosine-specific tRNA methyltransferases from Saccharomyces cerevisiae
… functional m$\sbsp{2}{2}$Gtase, was clone and sequenced. Based on the wild-type TRM1 sequence, oligonucleotides were designed and the mutant trm1 gene was isolated from SN1015-2a genomic DNA by polymerase chain reaction (PCR). Sequence comparison to the wildtype TRM1 gene revealed 14 silent …
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An Assessment of Potential False Positive E.coli Pyroprints in the CPLOP Database
… relies on the small variation of DNA sequences within the same species to develop a unique, reproducible fingerprint. By simultaneously pyrosequencing multiple polymorphic loci within the ribosomal operons known as the intergenic transcribed spacers, a reproducible output is obtained, …
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Homothallism in the Sordariaceae : Mating-type loci in selected species of Neurospora, Anixiella, and Gelasinospora
… in Neurospora, those with only the A-specific sequence (the majority) and those with both the A-specific and "a"-specific sequence (Neurospora terricola). Neurospora terricola and a number of homothallic Gelasinospora and Anixiella species are self-fertile but harbour both A and "a" idiomorphs …
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Molecular characterization of viruses infecting potato and vegetables in Iraq
… from PCR/RT-PCR and RCA were cloned and sequenced and data obtained were used for sequence analyses. The above approach led to the first molecular characterisation of three potyviruses; Potato virus Y (PVY), Bean yellow mosaic virus (BYMV) and Zucchini yellow mosaic virus (ZYMV), one …
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Decoding Human T Cell Immunity With Single-Cell Multi-Omics
… T cell gene expression and T cell receptor (TCR) sequence modalities. Across several longitudinal infectious disease studies, I identify transient T cell states after infection and link these phenotypes with specific TCR sequences. In the first chapter, I provide a comprehensive overview of the …
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