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 15 of 15 for “"homology search"”.
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Structural RNA Homology Search and Alignment Using Covariance Models
… CMs) are powerful computational tools for homology search and alignment that score both the conserved sequence and secondary structure of an RNA family. However, due to the high computational complexity of their search and alignment algorithms, searches against large databases and alignment …
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Single molecule fret study on the mechanism of RecA mediated strand exchange
… filament on single stranded (ss) DNA that searches for homology and exchanges complementary base pairs with a homologous double strand (ds) DNA to form a new heteroduplex. The study of strand exchange in ensemble assays is limited by the diffusion limited homology search process which masks …
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Fluorescence imaging of single molecule dynamics on long single stranded DNA
… of the following three proteins: (1) the DNA homology search on Escherichia coli (E. coli) RecA filaments formed on ssDNA, (2) the unidirectional motion of E. coli UvrD helicase and (3) the diffusion of E. coli single-stranded DNA binding protein (SSB). We observed that the homology search of …
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State-of-the-art Approaches for Sequencing, Assembling and Annotating Naphthenic Acid Degrading Bacterial Metagenomes
… protein structure prediction and structure homology search tools, which greatly enrich annotations of novel sequences that are below the threshold for homology finding by sequence alone. Overall, these approaches unveiled a diverse and constantly changing consortium of novel bacteria and …
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Novel Algorithms for Structural Alignment of Non-coding RNAs
… alignment is used as the basis for a structural search filter. This is combined with other filtering techniques and high-performance implementations to increase the practical speed of high-sensitivity search. As a whole, these improvements provide a foundation for and point toward future …
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Improving Profile Similarity Search and Alignment of Protein Sequences
… similar functional sites. Current sequence-based homology search methods are still unable to detect many similarities evident from protein spatial structures. We present a new method, COMPADRE, to assess the relationship between the query sequence and a hit in the database by considering the …
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Role Of The Pkna And Pknb Kinases In Mycobacterium Tuberculosis
… PknA/PknB. First approach is based on proteomic search by over-expressing PknA/PknB in M. tuberculosis. Proteomic search led to identification of proteasome to be a substrate of PknA and PknB in M. tuberculosis. Furthermore, I demonstrate that the phosphorylation of PrcA and PrcB by PknA …
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Biochemical and towards structural characterization of RAD51 and RAD51AP1 complexes
… catalyses key HRR steps of strand invasion and homology search in the sister chromatid. A large number of accessory factors and RAD51 binding proteins, with inherited mutations in many of these predisposing to cancer, regulate the activities of RAD51 and the RAD51 filament to promote or inhibit …
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The Role of Axl and Axl-like Proteins in Murine Spermatogenesis
… cells in the seminiferous epithelium. A sequence homology search identified an uncharacterized protein, AXL-LIKE, which we hypothesize is an endogenous dominant-negative of AXL. The structure of AXL-LIKE is essentially identical to AXL in the extracellular domain, but the intracellular portion of …
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Interrogation and engineering of RAD51:BRC repeat interactions
… with the broken ends, and allows efficient homology search. RAD51 is a promising therapeutic target in oncology. BRCA2 is a crucial mediator of RAD51 function and interacts with RAD51 through a set of 8 BRC repeats. A BRC repeat consists of two modules, an FxxA and an LFDE module, each …
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On the use of locality aware distributed hash tables for homology searches over voluminous biological sequence data
… analytics routines such as DNA and protein homology searches; these must also preferably be done in real-time. This thesis proposes a scalable and similarity-aware distributed storage framework, Mendel, that enables retrieval of biologically significant DNA and protein alignments against a …
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Molecular Studies of KpnAI and KpnBI R-M Systems : in KLEBSIELLA PNEUMONIAE M5a1 and GM236
… sequence in the GenBank database. However, a homology search of the amino acid sequence scored highly with <em>Eco</em>R124/3I, a type IC restriction enzyme. After alignment of the two proteins, two ATP binding domains, a DNA binding domain and seven helicase motifs were found. Eight small …
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Design and Discovery of Novel Bacteriocins
… of sequence-based and structure-based homology search strategies, dramatically increasing our knowledge of 4-HB Bacteriocins over the small numbers that had been previously reported. Additionally, methods for the generation of non-natural sequences were also explored, including the …
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Cellular responses to external threats probed by super-resolution microscopy
… break, supporting the idea that RecA mediates homology search. We report that RecA also forms bundles in the SOS response, and these bundles are ribbon-like structures, i.e. flat at one side and wide at the other side, hypothetically wrapping around DNA damaged sites. The conventional approach …
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Harnessing Deep Learning with Protein Language Models to Unveil Microbial Enzyme Function in Health and Disease
… many amino acid sequences or using sequence homology tools like BLAST, which employs a pairwise alignment strategy between query and target sequences. Advancements in deep learning have significantly aided the functional annotation of proteins and comprehension of their diverse functions. …