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 17 of 17 for “"Alignment-free"”.
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Establishing a Trustworthy First Approximation for Evolutionary Distances
… Traditionally, phylogenetic analysis relies on alignments of orthologs, but defining orthologs and separating them from paralogs is a complex task that may not always be suited to the large datasets of the future. An alternative to traditional, alignment-based approaches are whole-genome, …
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Developing computational methods to enhance understanding in glioma progression
… The latter part of the thesis presents an alignment-free method as an opportunity to quickly obtain an overview of pre-alignment sequencing data. Alignment-free sequence comparison is a method which has been in development in a wider biological context since the 1970s. However, thus far it …
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Alignments and beyond: A versatile swarm-based framework for de novo amplicon clustering
… variety of methods, many popular tools are alignment-based and employ a de novo clustering approach with a fixed global clustering threshold. More recently, Swarm introduced an alternative de novo clustering method, which uses a local clustering threshold in order to iteratively extend the …
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Prostate cancer evolution employing artificial intelligence to enhance biomarker discovery
… tools can assess intra-tumour heterogeneity via alignment-free methods and identify novel prostate cancer biomarkers associated with advanced disease across these different levels.<br/><br/>Exploring isolated prostate cellular sub-populations allows for novel biomarkers and targetable pathways to …
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Deep Learning for Taxonomy Prediction
… as the core algorithm in a compositional,alignment-free approach to taxonomy prediction.
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Integrated erbium lasers in silicon photonics
… by using an erbium trench. The approach is alignment free and allows the erbium-doped film deposition to be the last backend process, providing a pathway to a scalable CMOS compatible laser device.
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Computational methods for functional interpretation of diverse omics data
… computational tool, Carnelian, for robust, alignment-free functional profiling of whole metagenome sequencing reads, that is uniquely suited to finding hidden functional trends across diverse data sets in comparative analysis. Carnelian can find shared metabolic pathways, concordant …
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Fully Integrated CMOS-compatible mode-locked lasers
… potentially replaced with compact, power-ecient, alignment-free, cost-effectively mass-produced integrated photonics components. An on-chip high repetition-rate mode-locked laser is a key enabler of many integrated photonics applications, such as all-optical sampling, on-chip frequency combs, low …
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A Fast-Graph Approach to Modeling Similarity of Whole Genomes
… to approximate computationally expensive, full alignment comparison methods. Recent advances in next generation sequencing are providing a number of large whole-genome sequence datasets stemming from globally distributed disease occurrences. This offers an unprecedented opportunity for …
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DeepARG+ - A Computational Pipeline for the Prediction of Antibiotic Resistance
… new ARGs are predicted by making sequence alignment and calculating sequence similarity to existing ARG reference databases, which can be very time consuming. Here we introduce an alignment free and deep learning prediction method that incorporates both the primary protein sequences of ARGs …
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Optical Fiber Microstructures for Self-Contained Whispering Gallery Mode Excitation
… The press fit spherical resonator offers an alignment-free and conveniently pigtailed WGM coupler that has great potential for bio-science sensing applications and studies of resonant bispheres.
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Tackling the current limitations of bacterial taxonomy with genome-based classification and identification on a crowdsourcing Web service
… algorithms are based on a combination of the alignment-based algorithm BLASTN and the alignment-free method Sourmash, which is based on k-mers, and the MinHash algorithm. The potential of LINbase is shown by using examples of plant pathogenic bacteria.
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Towards a Complete Transcriptional Regulatory Code: Improved Motif Discovery Using Informative Priors
… sites are generally located in nucleosome-free regions. We use nucleosome occupancy predictions to compute a novel positional prior that biases the search towards the more accessible regions, thereby enriching the motif signal.</p><p>* Functional elements are often conserved across related …
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Variation-aware algorithms for cancer genome analysis
… This information is rarely used during read alignment and variant calling because of a lack of algorithms for doing so. Rediscovering these variants wastes significant computational time and negatively impacts the sensitivity of detection, motivating the development of new solutions. The …
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Long read mapping at scale: Algorithms and applications
… potential of long-read sequencers. Mapping and alignment of reads to a reference is typically the first step in genomics applications. Though long read technologies are still evolving, research efforts in bioinformatics have already produced many alignment-based and alignment-free read mapping …
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Germline variants associated with alternative splicing in colonic mucosa
… Transcript expression was quantified with the alignment-free Salmon algorithm. Two separate approaches with complementary methodologies were used to identify sQTLs: the sQTLseekeR package which analyses whole transcripts, and the Leafcutter package which infers changes in intron usage. Between …
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Comparative Analysis of Genomic Similarity Tools in Species Identification
… leveraging four bioinformatics tools: alignment-based methods (pyANI, Fas- tANI) and k-mer-based methods (Sourmash, BinDash 2.0). The analysis focuses on high- quality genomic datasets characterized by 100% completeness, ensuring consistency and accuracy in the comparison process. The …