ProteoVision Data

Phylogeny (DESIRE)

The subset of 152 species from the DESIRE (Sparse and Efficient Representation of Extant Biology), database was organized into a phylogenetic browser using a tree topology from the Banfiled lab.

Alignments

Each ribosomal RNA has an associated MSA. The alignments were generated accodring to procedure desribed at (https://doi.org/10.1093/molbev/msy101)

2D maps

Topologies of the protein secondary structures (Laskowski; 10.1093/nar/gkn860) were exported into PDB topology viewer using the EMBL-EBI PDBe API.

3D Structures

3D structures were fetched from the PDBe using the APIs of EMBL-EBI coordinate server. The selection of ranges was implemented using the syntax of the LiteMol’s coordinate server.

Secuence and structure associated data (Chemical modifications, Protein Contacts)

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Available attributes for calculated mapping data:

Nucleotide frequencies

Nucleotide frequencies in each column of an MSA were adjusted for presence of gaps. Thus, the gap frequencies were prorated and were treated as a uniform distribution among all possible amino acid characters, such that a single character in a gap counts as 0.05, as described by Bernier et al..

Shannon Entropy

The Shannon entropy (as well as all properties listed below) was computed from the gap adjusted probabilities as:

Two group comparison (TwinCons)

In case of two groups selected in the phylogeny browser, RiiboVision2.0 provides an additional option to compute an in house developed score, TwinCons. TwinCons ( https://doi.org/10.1371/journal.pcbi.1009541) is computed for a single position of the MSA that compares two pre-defined groups (represented by vectors of the gap adjusted nucleotide frequencies) based on their similarity defined by the pre-computed substitution matrix, blastn (https://github.com/LDWLab/TwinCons). TwinCons represents the transformation price between the two vector columns related by the substitution matrix.

Color Schemes

Each calculated attribute is mapped on a matplotlib colorscheme. For single continuum attributes (like Shannon entropy), RiboVision2.0 uses single continuum colormaps like plasma and viridis. For diverging data attributes (likeTwinCons), RiboVision2.0 uses diverging colormaps like Blue-White-Red. All colormaps were generated with the python matplotlib library and exported to JavaScript with the js-colormaps package. Further information about colormaps in matplotlib.