Animating and exploring phylogenies with fibre plots.
Ontology highlight
ABSTRACT:
SUBMITTER: Pearse WD
PROVIDER: S-EPMC5389409 | biostudies-literature |
REPOSITORIES: biostudies-literature
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Project description:MotivationClinicians, health officials and researchers are interested in the epidemic spread of pathogens in both space and time to support the optimization of intervention measures and public health policies. Large sequence databases of virus sequences provide an interesting opportunity to study this spread through phylogenetic analysis. To infer knowledge from large phylogenetic trees, potentially encompassing tens of thousands of virus strains, an efficient method for data exploration is required. The clades that are visited during this exploration should be annotated with strain characteristics (e.g. transmission risk group, tropism, drug resistance profile) and their geographic context.ResultsPhyloGeoTool implements a visual method to explore large phylogenetic trees and to depict characteristics of strains and clades, including their geographic context, in an interactive way. PhyloGeoTool also provides the possibility to position new virus strains relative to the existing phylogenetic tree, allowing users to gain insight in the placement of such new strains without the need to perform a de novo reconstruction of the phylogeny.Availability and implementationhttps://github.com/rega-cev/phylogeotool (Freely available: open source software project).Contactphylogeotool@kuleuven.be.Supplementary informationSupplementary data are available at Bioinformatics online.
| S-EPMC5860094 | biostudies-literature
Project description:Comparative genome- and proteome-wide screens yield large amounts of data. To efficiently present such datasets and to simplify the identification of hits, the results are often presented in a type of scatterplot known as a volcano plot, which shows a measure of effect size versus a measure of significance. The data points with the largest effect size and a statistical significance beyond a user-defined threshold are considered as hits. Such hits are usually annotated in the plot by a label with their name. Volcano plots can represent ten thousands of data points, of which typically only a handful is annotated. The information of data that is not annotated is hardly or not accessible. To simplify access to the data and enable its re-use, we have developed an open source and online web tool with R/Shiny. The web app is named VolcaNoseR and it can be used to create, explore, label and share volcano plots ( https://huygens.science.uva.nl/VolcaNoseR ). When the data is stored in an online data repository, the web app can retrieve that data together with user-defined settings to generate a customized, interactive volcano plot. Users can interact with the data, adjust the plot and share their modified plot together with the underlying data. Therefore, VolcaNoseR increases the transparency and re-use of large comparative genome- and proteome-wide datasets.
| S-EPMC7689420 | biostudies-literature
Project description:0dpa Fibre vs epidermal laser capture microdisection comparison Keywords: Development
2006-06-27 | GSE5133 | GEO
Project description:Generating the raw data for a de novo genome assembly project for a target eukaryotic species is relatively easy. This democratization of access to large-scale data has allowed many research teams to plan to assemble the genomes of non-model organisms. These new genome targets are very different from the traditional, inbred, laboratory-reared model organisms. They are often small, and cannot be isolated free of their environment - whether ingested food, the surrounding host organism of parasites, or commensal and symbiotic organisms attached to or within the individuals sampled. Preparation of pure DNA originating from a single species can be technically impossible, but assembly of mixed-organism DNA can be difficult, as most genome assemblers perform poorly when faced with multiple genomes in different stoichiometries. This class of problem is common in metagenomic datasets that deliberately try to capture all the genomes present in an environment, but replicon assembly is not often the goal of such programs. Here we present an approach to extracting, from mixed DNA sequence data, subsets that correspond to single species' genomes and thus improving genome assembly. We use both numerical (proportion of GC bases and read coverage) and biological (best-matching sequence in annotated databases) indicators to aid partitioning of draft assembly contigs, and the reads that contribute to those contigs, into distinct bins that can then be subjected to rigorous, optimized assembly, through the use of taxon-annotated GC-coverage plots (TAGC plots). We also present Blobsplorer, a tool that aids exploration and selection of subsets from TAGC-annotated data. Partitioning the data in this way can rescue poorly assembled genomes, and reveal unexpected symbionts and commensals in eukaryotic genome projects. The TAGC plot pipeline script is available from https://github.com/blaxterlab/blobology, and the Blobsplorer tool from https://github.com/mojones/Blobsplorer.
| S-EPMC3843372 | biostudies-literature
Project description:0dpa Fibre vs epidermal laser capture microdisection comparison Total RNA was isolated from each cell type (fibre initial or non-fibre epidermal pavement cell) from both Plant 1 and Plant 2. Hence, there were two biological replicates of each cell-type. Sub-samples of each cell type, designated here as technical replicates, were taken as separate batches of cells from different groups of ovules, but each from the same pair of plants. In particular, there were four sub-samples of fibre initial cells from plant 1 and two from plant 2 and two sub-samples of non-fibre epidermal from plant 1 and four from plant 2. The complete experiment involved three dye-swap pairs using a total of 6 arrays.
2006-06-26 | E-GEOD-5133 | biostudies-arrayexpress
Project description:Environmental long read amplicons of soil fungi across Podzol soil profile
| PRJEB32949 | ENA
Project description:Flight feathers have evolved under selective pressures to be sufficiently light and strong enough to cope with the stresses of flight. The feather shaft (rachis) must resist these stresses and is fundamental to this mode of locomotion. Relatively little work has been done on rachis morphology, especially from a mechanical perspective and never at the nanoscale. Nano-indentation is a cornerstone technique in materials testing. Here we use this technique to make use of differentially oriented fibres and their resulting mechanical anisotropy. The rachis is established as a multi-layered fibrous composite material with varying laminar properties in three feathers of birds with markedly different flight styles; the Mute Swan (Cygnus olor), the Bald Eagle (Haliaeetus leucocephalus) and the partridge (Perdix perdix). These birds were chosen not just because they are from different clades and have different flight styles, but because they have feathers large enough to gain meaningful results from nano-indentation. Results from our initial datasets indicate that the proportions and orientation of the laminae are not fixed and may vary either in order to cope with the stresses of flight particular to the bird or with phylogenetic lineage.
| S-EPMC4223922 | biostudies-literature
Project description:BackgroundIt is often desirable to observe how a disease progresses over time in individual patients, rather than graphing group averages; and since multiple outcomes are typically recorded on each patient, it would be advantageous to visualise disease progression on multiple variables simultaneously.MethodsA variety of vector plots and a path plot have been developed for this purpose, and data from a longitudinal Huntington's disease study are used to illustrate the utility of these graphical methods for exploratory data analysis.ResultsInitial and final values for three outcome variables can be easily visualised per patient, along with the change in these variables over time. In addition to the disease trajectory, the path individual patients take from initial to final observation can be traced. Categorical variables can be coded with different types of vectors or paths (e.g. different colours, line types, line thickness) and separate panels can be used to include further categorical or continuous variables, allowing clear visualisation of further information for each individual. In addition, summary statistics such as mean vectors, bivariate interquartile ranges and convex polygons can be included to assist in interpreting trajectories, comparing groups, and detecting multivariate outliers.ConclusionVector and path plots are useful graphical methods for exploratory data analysis when individual-level information on multiple variables over time is desired, and they have several advantages over plotting each variable separately.
| S-EPMC2693505 | biostudies-literature
Project description:ObjectivesTo explore the optimal laser settings and treatment strategies for thulium fibre laser (TFL) lithotripsy, namely, those with the highest treatment efficiency, lowest thermal injury risk, and shortest procedure time.Materials and methodsAn in vitro kidney model was used to assess the efficacy of TFL lithotripsy in the upper calyx. Stone ablation experiments were performed on BegoStone phantoms at different combinations of pulse energy (EP ) and frequency (F) to determine the optimal settings. Temperature changes and thermal injury risks were monitored using embedded thermocouples. Experiments were also performed on calcium oxalate monohydrate (COM) stones to validate the optimal settings.ResultsHigh EP /low F settings demonstrated superior treatment efficiency compared to low EP /high F settings using the same power. Specifically, 0.8 J/12 Hz was the optimal setting, resulting in a twofold increase in treatment efficiency, a 39% reduction in energy expenditure per unit of ablated stone mass, a 35% reduction in residual fragments, and a 36% reduction in total procedure time compared to the 0.2 J/50 Hz setting for COM stones. Thermal injury risk assessment indicated that 10 W power settings with high EP /low F combinations remained below the threshold for tissue injury, while higher power settings (>10 W) consistently exceeded the safety threshold.ConclusionsOur findings suggest that high EP /low F settings, such as 0.8 J/12 Hz, are optimal for TFL lithotripsy in the treatment of COM stones. These settings demonstrated significantly improved treatment efficiency with reduced residual fragments compared to conventional settings while keeping the thermal dose below the injury threshold. This study highlights the importance of using the high EP /low F combination with low power settings, which maximizes treatment efficiency and minimizes potential thermal injury. Further studies are warranted to determine the optimal settings for TFL for treating kidney stones with different compositions.
| S-EPMC10947524 | biostudies-literature