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PhyloProfileCorona

The data of PhyloProfile Corona is displayed for an interactive exploration of the feature-aware phylogenetic profile of isolates from the Coronaviridae family. This is a lite version of PhyloProfile, which is pre-configured only for its use with the Coronavirus data.

Table of Contents

Usage

Feature-aware phylogenetic profile of the SARS-CoV-2 protein set (GCF_009858895.2) across the Coronaviridae family.

  • Taxa (x-axis) are ordered with increasing evolutionary distance to SARS-CoV-2. The dataset covers samples in the respective order from betacoronaviruses (Sarbecovirus, Hibecovirus, Nobecovirus, Merbecovirus, and Embecovirus), alpha-, gamma-, and deltacoronaviruses.
  • Rows indicate the reference protein set of SARS-CoV-2, which comprises core proteins, accessory proteins, and polyprotein components. Abbreviations: M – membrane glycoprotein, N – nucleocapsid protein, S – spike glycoprotein, E – envelope protein, ORF - open reading frame, NSP - non-structural protein.
  • Dots indicate orthologs of each protein in the respective isolate. To inspect the domain architecture comparison between the protein in SARS-CoV-2 and the one from the datapoint, click on the dot, select detailed plot, select the ortholog from the barplot, and click on show domain architecture.
  • The color scheme represents the similarity of annotated features between SARS-CoV-2 proteins and the respective orthologs using the FAS scores (Koestler, et al. 2010) by assigning values between 0 and 1. The score is penalized for missing features (FAS_F; dot color) and added features (FAS_B; background color) in the orthologous protein. For instance, a protein with an identical feature architecture to the reference protein in SARS-CoV-2 would have FAS_F = 1 and FAS_B = 1, and would appear as a blue dot in a light-grey background according to the color scale.
  • For further details on the biological interpretation of the data, please refer to the article The evolutionary making of SARS-CoV-2.

Bugs

Any bug reports or comments, suggestions are highly appreciated. Please open an issue on GitHub or be in touch via email.

License

This tool is released under MIT license.

Contact

Ingo Ebersberger [email protected]