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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 17 of 17 for “"multiple alignment"”.
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Multiple Alignment of Structures using Center of Proteins
… the area of computational methods for aligning multiple protein structures. As the problem under consideration is known to be np–complete, several ways for coming up with good approximations have been suggested over the years. A new approach for achieving better, or at least as good results as …
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Investigation of the Conservation of Biological Function in Transposable Elements using a Multiple Alignment Strategy
… than non-functional regions and leveraged multiple novel approaches and datasets to study this hypothesis. However, when compared to coding regions, the conservation patterns of TEs are harder to detect as they are younger sequences found in fewer species. This makes exploration of …
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Microarray time-series data clustering via gene expression profile alignment
… clustering methods introducing the concept of multiple alignment of natural cubic spline representations of gene expression profiles are presented. The multiple alignment is achieved by minimizing the sum of integrated squared errors over a time-interval, defined on a set of profiles. The …
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Computational approaches to modeling the conserved structural core among distantly homologous proteins
… structures themselves. Namely, we introduce the multiple alignment algorithm Matt (Multiple Alignment with Translations and Twists), an aligned fragment pair chaining algorithm that, in intermediate steps, allows local flexibility between fragments. Matt temporarily allows small translations and …
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Probabilistic Model-Based Approach to Evolutionary Analysis of Non-Coding Sequences
… to analyze non-coding sequences by comparing multiple genomes from different species. The success of comparative genomic studies relies on bioinformatics tools that aid the comparison and analysis of genome sequences. Here, we propose and develop computational tools to evolutionarily analyze …
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The Role of Nogo-A During Development of the Chick Central Nervous System
… undescribed Nogo-A specific regions from multiple alignment of divergent species. The <em>Nogo</em> gene is differentially expressed during development and we identified a secondary <em>Nogo-A</em> splice variant. <em>In situ</em> hybridization found <em>Nogo-A</em> induction to be …
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Error correcting optical mapping data
… to dealing with insertion and deletions in the alignment of long reads. Moreover, they are arguably harder since the data is integral and susceptible to inaccuracy. We develop cOMet to tackle error correct Rmap data, which to the best of our knowledge is the is the only non-proprietary error …
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Implications of Nanofiber Length and Polydispersity on Flow Alignment
… a compelling system for studying flow-induced alignment, a key factor in designing bio-based materials with tailored properties. While structural properties of PNFs are at rest well-characterized, comprehensive insight into their colloidal behavior, shear response, and alignment mechanisms …
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Alignment, Clustering and Extraction of Structured Motifs in DNA Promoter Sequences
… boxes may not be exact copies, but may have multiple mismatched positions. The challenge is extenuated by the lack of resources for real datasets covering a wide range of possible cases. Also, incomplete annotation of real data leads to the discovery of unknown motifs that may be regarded as …
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Alignment- and Alignment-refining Algorithms: Effects on Branch-length Estimation and Selection Pattern Analyses
… consists of a study of the effects of multiple-alignment method on phylogenetic analyses. First, I investigated the effects of multiple-sequence alignment quality on branch-length estimation, which can influence downstream bioinformatic analyses such as estimating rates of evolution and …
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Comparative microbial genome analysis of lactobacilli
… of strains of L. salivarius. We found that multiple phylogenomic and non-phylogenomic methods used for reconstructing trees all converge on similar tree topologies, showing that different metrics largely agree on the evolutionary history of the species. The greatest genomic variation lies on …
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The impact of EPHA2 polymorphism on KSHV infectivity and KS prevalence among HIV/AIDS patients in South Africa
… these sequences to the NCBI reference by multiple alignment. A number of variants were identified throughout the EPHA2 coding region and assessed statistically for association with KSHV susceptibility and/or KS prevalence. A novel heterozygous transition (c.2727C>T), which is predicted to …
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Machine Learning Approaches for Modeling and Correction of Confounding Effects in Complex Biological Data
… data. An observed sample could be the mixture of multiple underlying sources and we may be only interested in one or part of the sources. The second type of complexities come from the acquisition process of the data. Different samples may be gathered at different time and/or from different …
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Data mining in computational proteomics and genomics
… detection problem is to locate all peaks across multiple window sizes of interest in the dataset. A new method, called PeakID, is proposed in this dissertation, which solves the elastic peak detection problem in 2D LC-MS data without yielding any false negative. PeakID employs a novel data …
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Algorithms for estimating rates of nucleotide change
… substitution rates between species from multiple sequence alignments. To address the problem of estimating mutation rates within species, Vogl (2014) has developed a general algorithm for the case of bi-allelic neutral evolution. A necessary first step in generalizing the Vogl estimator …
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Algorithms for estimating rates of nucleotide change
… substitution rates between species from multiple sequence alignments. To address the problem of estimating mutation rates within species, Vogl (2014) has developed a general algorithm for the case of bi-allelic neutral evolution. A necessary first step in generalizing the Vogl estimator …
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On-board Robotic Multi-pinhole SPECT System for Region-of-interest (ROI) Imaging
… (LINAC), patient table and patient.</p><p>An alignment method was developed in this work to calibrate the on-board robotic SPECT to the LINAC coordinate frame and to the coordinate frames of other on-board imaging systems such as CBCT. This alignment method utilizes line sources and one …