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 201 for “"Sequence-Similarity"”.
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Assessing the Role of Clusters Derived from Large Sequence Similarity Networks for Gene Function Predictions
… efforts have resulted in a massive inflow of raw sequence data. This raw data, when appropriately processed and analyzed, can provide insight to a trained biologist and aid in hypothesis-driven research. Given the time and resource requirements necessary for biological experiments, computational …
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Identification of novel transcripts in hepatocellular carcinoma using RNA-seq
… Firstly, I identified function ontology for high sequence similarity gene sets of each novel transcript. Similarity genes had significant enriched function in regulation of transcription and regulation of RNA metabolic process. And I confirmed that the expressions of the candidate genes were …
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Community Classification of the Protein Universe
… to be performed by the community of protein sequence similarity search users. In the first chapter, I review the history of protein sequence and protein family databases, and how the abstract concept of a protein family is expressed as a computational model. I review in greater detail the …
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Homology-Based Functional Proteomics By Mass Spectrometry and Advanced Informatic Methods
… isolated protein with a specific gene or protein sequence in silico, thus inferring its specific biochemical function based upon previous characterizations of that protein or a similar protein having that sequence identity. By performing this analysis on a large scale in conjunction with …
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A study of the phylogenetics, nutrition and one-carbon metabolism of Syntrophococcus sucromutans
… the Eubacteria, by virtues of 16S ribosomal RNA sequence similarity analysis. It is part of a well defined genealogic entity described as the Butyrivibrio subdivision which, like the Sporomusa subdivision contains both ultrastructurally Gram-positive and Gram-negative bacteria.
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Gene discovery and expression profilng in the toxin-producing marine diatom, Pseudo-nitzschia multiseries (Hasle) Hasle
… DNA (cDNA) library and a database of expressed sequence tags (ESTs) for P. multiseries 2552 cDNAs were sequenced, generating a set of 1955 unique contigs, of which 21 % demonstrated significant similarity with known protein coding sequences. Among the genes identified by sequence similarity were …
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Algorithmic Developments for Sequence Analysis, Structure Modeling and Functional Prediction of Proteins
Sequence, structure and function, being the three most important properties of proteins, are interrelated through homology relationships. In this post-genome era, we are equipped with abundant sequence information. Homology inference is thus of great practical importance because of its ability to …
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The tangled history of olfaction in African mole-rats, Bathyergidae: insights from Olfactory Receptor genes
… Using a PCR-sequencing approach, 178 unique OR sequences, corresponding to 119 unique OR genes are characterised from 14 mole-rat species. Bathyergidae OR genes are classified using sequence similarity and phylogenetic comparison with more than 50 mammalian OR subgenomes.
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Identification of the virulence gene of Mycobacterium tuberculosis
… by grouping the proteins into families based on sequence similarity with the aid of BLASTP and the NCBI BLASTClust program.
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Sequence characterization of the HSA12/22/12 evolutionary breakpoint region on SSC5q21
… breakpoint region on SSC5q21 has been sequenced, further localized, and preliminarily characterized. The existence and location of the breakpoint regions were originally determined in the human-porcine comparative map constructed by Meyers and colleagues. Bacterial artificial chromosome …
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Entropy Measurements and Ball Cover Construction for Biological Sequences
… is making it easier to select or engineer DNA sequences that produce dangerous proteins, it is important to be able to predict whether a novel DNA sequence is potentially dangerous by determining its taxonomic identity and functional characteristics. These tasks can be facilitated by the ever …
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Gene discovery and expression profiling in the toxin-producing marine diatom, Pseudo-nitzschia multiseries (Hasle) Hasle
… DNA (cDNA) library and a database of expressed sequence tags (ESTs) for P. multiseries. 2552 cDNAs were sequenced, generating a set of 1955 unique contigs, of which 21% demonstrated significant similarity with known protein coding sequences. Among the genes identified by sequence similarity were …
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Laccases from actinomycetes for lignocellulose degradation
… 30 and 37oC. Analysis of the 16S rRNA gene sequences of the strains showed that strain MS26 had the highest sequence similarity (99%) to Streptomyces atrovirens strain NRRL B-16357 and Streptomyces viridodiastaticus strain IFO 13106. Strain DFNR17 had the highest 16S rRNA gene sequence …
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Graphical methods in RNA structure matching
… RNA structures may have little or no detectable sequence similarity, making the identification of conserved RNAs difficult. This is a particularly serious problem when studying regulatory structures in RNA. In many cases, such as that of cellular internal ribosome entry sites, although we can …
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Studies of verticillium wilt and characterization of candidate verticillium wilt resistance genes in the mint species Mentha longifolia (L) Huds
… genes. The mint RGAs shared predicted amino acid sequence similarity with disease resistance genes and RGAs from various other plant species, and were grouped into seven distinct families based on DNA and predicted amino acid sequence similarity. In addition to the NBS-related RGAs, a fragment of …
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Molecular cloning of three genes encoding SNF1/AMPK protein kinases from Drosophila melanogaster.
… polypeptides share intermediate levels of sequence similarity with SNF1 but share higher levels of sequence similarity with the putative human protein kinase KP78, a marker protein lost in chemically induced primary carcinoma of the pancreas. The third Drosophila protein kinase gene …
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Isolation and Characterization of a Novel Gene, xMADML, Involved in Xenopus Laevis Eye Development Using Cornea -Lens Regeneration
… of its embryonic expression pattern and its sequence similarity to human NRBP and mouse MADM genes. This gene, xMADML, was characterized through molecular analysis, which showed both similarity and important differences to MADM, and protein knock-down, which showed that xMADML is necessary in …
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Characterization of XV7 and XV9 cDNA clones which confer osmotolerance to Eschericia coli
The sequence similarity between XV7 and the mammalian syntaxin-like protein kinase receptor shows that XV7 may function similar to that of animal protein kinases. The syntaxin-like protein kinase receptor was recently entered into the Genbank (Thoreau, unpublished), therefore not much is known …
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Structure-based realignment of non-coding RNAs in multiple whole genome alignments
… have become a central tool in biological sequence analysis. A major application is the de novo prediction of non-coding RNAs (ncRNAs) from structural conservation visible in the alignment. However, current methods for constructing genome alignments do so by explicitly optimizing for …
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A bioinformatic study of the 5' upstream region of the human gene
… a key issue in biology. There is much non-coding sequence upstream of the human gene, a small proportion of which is regulatory. The aim of this project is to gain a better understanding of organisation, structure and function of this region via large-scale sequence studies. The 10Kb 5' upstream …
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