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 127 for “"Sequence alignment"”.
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Integrated multiple sequence alignment
… enhancements for automated and manual multiple sequence alignment: existing alignment algorithms are made more easily accessible and new algorithms are designed for difficult cases. Firstly, we introduce the QAlign framework, a graphical user interface for multiple sequence alignment. It …
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CSA-X: Modularized Constrained Multiple Sequence Alignment
Imposing additional constraints on multiple sequence alignment (MSA) algorithms can often produce more biologically meaningful alignments. Hence, various constrained multiple sequence alignment (CMSA) algorithms have been developed in the literature, where researchers used anchor points, regular …
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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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Accelerating genomic sequence alignment using high performance reconfigurable computers
… reconfigurable computers to accelerate genomic sequence alignment specifically for genome sequencing applications. We present a highly optimized implementation of a parallel sequence alignment algorithm for the Berkeley Emulation Engine (BEE2) reconfigurable computer, allowing a single BEE2 to …
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Fast program for sequence alignment using partition function posterior probabilities
The key requirements of a good sequence alignment tool are high accuracy and fast execution. The existing Probalign program is a highly accurate tool for sequence alignment of both proteins and nucleotides. However, the time for execution is fairly high. The focus is therefore, to reduce the …
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Multiple sequence alignment with sequence length heterogeneity and its applications
Submission original under an indefinite embargo labeled 'Open Access'. The submission was exported from vireo on 2025-10-20 without embargo terms
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Large-scale methods for multiple sequence alignment and phylogeny estimation
… analyses generally involve passing genetic sequence data through a pipeline of transformations. These prominently include multiple sequence alignment (MSA) and phylogeny estimation, which are both core challenges in computational biology. Their established mathematical formulations are …
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Using structure to explore the sequence alignment space of remote homologs
… modeling by homology requires an accurate sequence alignment between the query sequence and its structural template. However, sequence alignment methods based on dynamic programming (DP) are typically unable to generate accurate alignments for remote sequence homologs, thus limiting the …
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Digitizing a Three-Dimensional Brain Atlas: Image Sequence Alignment and Volumetric Encoding
… section. However, the images in the raw image sequence are not aligned with each other and therefore must be spatially registered. This dissertation describes several new methods employed by the atlas construction process. The most important components of the image registration process are the …
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Improved GPU implementations of the Pair-HMM forward algorithm for DNA sequence alignment
The student, Enliang Li, accepted the attached license on 2021-04-30 at 13:30.
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An Efficient Primer Selection Process Combining Progressive and Iterative Multiple Sequence Alignment Strategies: ClustalW and HMMER
… algorithm to identify candidate DNA primer sequences. DNA sequencing primers are a critical element of polymerase chain reaction (PCR) and DNA sequence analysis. A variety of methods for deriving DNA primers exist, but such methods are often computationally intensive, or do not use available …
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Simulating recombinant sequence date to evaluate and improve computational methods of multiple sequence alignment and recombinant identification
… the evolutionary history of nucleotide sequences, and the accurate identification of recombinant sequences is particularly important in the context of downstream phylogenetics-based sequence analyses. Evaluating recombination detection methods requires the simulation of sequence data, …
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Analysis of the impact of sequencing errors on BLAST using fault injection
… the impact of sequencing errors in post-sequence computational analyses, including local alignment search and multiple sequence alignment. While the error rates of sequencing technology are commonly reported, the significance of these numbers cannot be fully grasped without putting them …
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Exact genome alignment
… task in these studies is to align the genome sequences accurately. Sequence alignment helps to identify regions of similarity between the sequences to establish their functional, evolutionary and structural relationship. The thesis investigates the performance of two sequence alignment …
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Co-linear Chaining on Graphs With Cycles
Sequence alignment by exact or approximate string matching is one of the fundamental problems in bioinformatics. As the volume of sequenced genomes grows rapidly, pairwise sequence alignment becomes inefficient for pan-genomic analyses involving multiple sequences. The graph representation of …
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Scrambling analysis of ciliates
… developed which attempts to model the problem of sequence alignment between scrambled and descrambled genes. With this system, sequences can be classified into relevant functional segments. It also provides a framework whereby we can compare various ciliate sequence alignment algorithms. After …
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Using Co-evolutionary Information to Improve Protein Language Modelling
… language model that conditions the target sequence on its multiple sequence alignment, allowing us to better model protein families.
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Matching Genetic Sequences in Distributed Adaptive Computing Systems
… found in the field of bioinformatics, is the DNA sequence alignment problem. This thesis presents a runtime reconfigurable FPGA implementation of the Smith-Waterman similarity comparison algorithm. Additionally, this thesis presents tools designed for the ACS API that assist developers creating …
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Estimating telomere length from whole genome sequencing data
… reads derived from interstitial telomere sequences means that it does not rely on previously applied analyses, a source of bias. The other tool described in this thesis is Parabam. Parabam is the first tool of its kind to allow users to apply a function to all of the reads in sequence …
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