Viruses and Bioinformatics from Virology.uvic.ca
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Viruses and Bioinformatics from Virology.uvic.ca
Virus and bioinformatics articles with some microbiology and immunology thrown in for good measure
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UniProt Protein Feature Viewer, a BioJS component

ProtVista is a comprehensive visualization tool for the graphical representation of protein sequence features in the UniProt Knowledgebase, experimental proteomics and variation public datasets. The complexity and relationships in this wealth of data pose a challenge in interpretation. Integrative visualization approaches such as provided by ProtVista are thus essential for researchers to understand the data and, for instance, discover patterns affecting function and disease associations.

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DNAism: exploring genomic datasets on the web with Horizon Charts

DNAism: exploring genomic datasets on the web with Horizon Charts | Viruses and Bioinformatics from Virology.uvic.ca | Scoop.it
Computational biologists daily face the need to explore massive amounts of genomic data. New visualization techniques can help researchers navigate and understand these big data. Horizon Charts are a relatively new visualization method that, under the right circumstances, maximizes data density without losing graphical perception.
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The Scale of the Universe - An Interactive Visual Understanding of How Small Viruses and Microorganisms Really Are

Zoom from the edge of the universe to the quantum foam of spacetime and learn about everything in between.
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GenVisR: Genomic Visualizations in R

Summary: Visualizing and summarizing data from genomic studies continues to be a challenge. Here, we introduce the GenVisR package to addresses this challenge by providing highly customizable, publication-quality graphics focused on cohort level genome analyses. GenVisR provides a rapid and easy-to-use suite of genomic visualization tools, while maintaining a high degree of flexibility by leveraging the abilities of ggplot2 and Bioconductor.

Availability and Implementation: GenVisR is an R package available via Bioconductor (https://bioconductor.org/packages/GenVisR) under GPLv3. Support is available via GitHub (https://github.com/griffithlab/GenVisR/issues) and the Bioconductor support website.
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Realtime analysis and visualisation of MinION sequencing data with npReader.

Abstract
MOTIVATION:

The recently released Oxford Nanopore MinION sequencing platform presents many innovative features opening up potential for a range of applications not previously possible. Among these features, the ability to sequence in real-time provides a unique opportunity for many time-critical applications. While many software packages have been developed to analyse its data, there is still a lack of toolkits that support the streaming and real-time analysis of MinION sequencing data.

RESULTS:

We developed npReader, an open-source software package to facilitate real-time analysis of MinION sequencing data. npReader can simultaneously extract sequence reads and stream them to downstream analysis pipelines while the samples are being sequenced on the MinION device. It provides a command line interface for easy integration into a bioinformatics work flow, as well as a graphical user interface which concurrently displays the statistics of the run. It also provides an application programming interface for development of streaming algorithms in order to fully utilize the extent of nanopore sequencing potential.

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Visualization of DNA synthesis in vivo

Visualization of DNA synthesis in vivo | Viruses and Bioinformatics from Virology.uvic.ca | Scoop.it
To visualize the synthesis of biomolecules in living organisms, artificial small molecules can be added to and incorporated by the cell's own biosynthetic machinery. Subsequently, the modified biomolecules containing the artificial units can be selectively labelled with fluorescent substances. Until now, this approach had one major limitation: the substances used for labelling were toxic and caused cell death.

 

Anne Neef, a PhD student from the Institute of Organic Chemistry at the University of Zurich, has developed a new substance that can replace the natural nucleoside thymidine in DNA biosynthesis. This fluorinated nucleoside called "F-ara-Edu" labels DNA with little or no impact on genome function in living cells and even whole animals. "F-ara-Edu" is less toxic than previously reported compounds used for DNA labelling and it can be detected with greater sensitivity.


Via Dr. Stefan Gruenwald
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