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Showing 1 to 10 of 10 for “"Bioinformatics pipelines"”.
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GOGO: An Improved Algorithm to Measure the Semantic Similarity Between Gene Ontology Terms
… (GO) terms is an essential step in functional bioinformatics research. We implemented a software named GOGO for calculating the semantic similarity between GO terms. GOGO has the advantages of both information-content-based and hybrid methods, such as Resnik’s and Wang’s methods. Moreover, GOGO …
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De Novo Assembly of Genomes in Microbiomes: From Amplicons to Whole-Genome Shotgun Sequencing
… However, a critical bottleneck in current bioinformatics investigations is the assembly of metagenome at the strain-level resolution. This is indispensable for gaining profound insights into microbial communities and addressing pivotal biological inquiries. Despite the availability of …
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Development of Models for the Action of Novel Anti-apoptotic Proteins using Gene Regulation, Pathway Analysis and Protein Structure Prediction
… Technology Ltd with the goal of using modern bioinformatics tools to analyse the major genetic and metabolic pathways involved in ovarian and non-small-cell lung carcinoma (NSCLC). The study also sought to characterise the predicted structures of some of the key proteins that regulate these …
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AUGMENTING SEQUENCING TECHNOLOGY FOR BETTER INFERENCE IN SOIL MICROBIOME ANALYSIS
… functional assignments, along with open-source bioinformatics pipelines has further empowered scientists to explore microbiomes in many environments. However, there are limitations to sequence data that have constrained the ecological inferences in microbiome research. One such limitation, the …
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Alignments and beyond: A versatile swarm-based framework for de novo amplicon clustering
… size of the data sets challenges the involved bioinformatics pipelines. Clustering sequences to, e.g., group those from related organisms is a common step in such processing pipelines but it is also a potential bottleneck preventing the full utilisation of the massive data sets. Over the years, …
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Decoding DNA: scalable genome annotation software, generative AI, and application to the cactus pear genome
… For example, existing genome annotation pipelines suffer from a lack of automation, an inability to control precision, and from poor performance in predicting alternative splicing.The goal of this work is to develop improved computational tools for genome annotation and to apply the …
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Metabarcoding pollen to identify allergenic species of grasses (Poaceae) and ragweed (Ambrosia spp.) across six monitored sites in South Africa
… pre-processed, and assigned to taxa using two bioinformatics pipelines. The first followed the method for analysing metabarcoding dualindex data described by Sickel et al. (2015), while the second was adapted from the National Botanic Garden of Wales Plant Illumina pipeline developed by Ford …
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Metabarcoding pollen to identify allergenic species of grasses (Poaceae) and ragweed (Ambrosia spp.) across six monitored sites in South Africa
… pre-processed, and assigned to taxa using two bioinformatics pipelines. The first followed the method for analysing metabarcoding dual- index data described by Sickel et al. (2015), while the second was adapted from the National Botanic Garden of Wales Plant Illumina pipeline developed by Ford …
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Applicability and limitations of transcriptomic pipelines in livestock species
… for a selected trait requires high-throughput bioinformatics pipelines to effectively filter and prioritize pertinent genes and transcripts. Livestock species represent a vital branch of the Tree of Life, serving as food sources, model organisms, and essential species within ecological niches. …
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Microbiome associated with Ulva lacinulata and seawater in an integrated abalone (Haliotis midae)–Ulva system with partial recirculation
… samples and compared commonly used bioinformatic pipelines for the 16S rDNA (QIIME2 vs. mothur) and ITS2 (PIPITS vs. QIIME2) genes to evaluate how different bioinformatics pipelines influence taxonomic classification and subsequent diversity analyses. In chapter 3, culture- dependent techniques …