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Showing 1 to 20 of 35 for “"Multiple sequence alignment"”.
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Integrated multiple sequence alignment
… presents 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. …
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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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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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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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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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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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Microbial degradation of high molecular weight polycyclic aromatic hydrocarbons
… of Stenotrophomonas maltophilia on the basis of multiple sequence alignment analysis of 16SrRNA gene sequences. Differentiation of the three strains was possible by pulse field gel electrophoresis and DNA:DNA hybridisation methods. The St. maltophilia strains had similar degradative profiles to …
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Genome-wide microbial phylogeny reconstruction with polytomy identification
… biology. With ever increasing speed of newly sequenced microbial genome deposition, the study of the evolutionary relationships among microbes has becoming more and more imperative. Using complete genome sequences to infer large scale multi-furcating microbial phylogeny without relying on MSA …
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Fine-tuning Boltz for Antibody-Antigen Binding Prediction
… in antibody and antigens. This thesis evaluates multiple strategies for improving predictive performance. First, we investigate a custom multiple sequence alignment (MSA) experiment. Standard Boltz-2 training relies on MSAs from broad protein databases, which capture global diversity but …
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Reconstructing Cross-Species Ancestral Adeno-Associated Viruses for Enhanced Gene Therapy Delivery
… a computational framework based on ancestral sequence reconstruction (ASR) to engineer synthetic ancestral AAV capsids with the goal of enhanced targeting specificity and potency. We first validated this computational framework by replicating the previously engineered Anc80L65 capsid. Then, …
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Phylogenetic Signals in Protein Data
… the discovery of coevolutionary signals in a multiple sequence alignment (MSA). Unlike methods which fold proteins using molecular dynamic (MD) simulations, these coevolutionary methods make use of correlation information to fold large protein structures orders of magnitudes faster. Often the …
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Protein structure determination using evolutionary information
… selection acts upon a gene to optimize its sequence to perform a task. For protein-coding genes, the task includes folding, stability, and function. The record of the evolutionary process, which in itself is probabilistic, is contained within a multiple sequence alignment. A statistical …
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Decomposition of Proteins into Functionally and Evolutionarily Independent Cooperative Units
… the correlations between positions in a multiple sequence alignment of a protein family. In this work, coupling analysis and experimental studies were used to analyze two protein families - the TonB dependent receptors and the S1A serine proteases. The TonB dependent receptor family …
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Probabilistic Model-Based Approach to Evolutionary Analysis of Non-Coding Sequences
Non-coding sequences, constituting a large fraction of genomic DNA, are of great importance because (i) they harbor functional elements that are involved in the regulation of gene expression and (ii) they are essential for the study of genome structure and evolution. The availability of genome …
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Methods for Analysis of Prokaryotic Genome Architecture
… there are more than 96,000 bacterial genomes sequenced and this number is rapidly increasing. Some closely related groups have large numbers of genomes sequenced creating interesting comparative challenges: E. coli more than 5,400 isolates, S. aureus almost 9,000. As this sampling through …
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Single Molecule Förster Resonance Energy Transfer and Super Resolution Force Spectroscopy Study of Elongation Factor G Evolution, Conformation, and Function
… hydrolysis, which may drive tRNA translocation. Multiple sequence alignment (MSA) of switch I identified a highly conserved threonine (Thr48) in prokaryotes, which may be homologous with Thr56 of eukaryotes. Two mutations were prepared: a phosphomimic (T48E) and a nonpolar substitution (T48V). …
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