Evolutionary Analysis of SARS-CoV-2 Proteome

Select any protein from the SARS-CoV-2 proteome to see evolutionary analysis

Nucleotide Position

Shows the evolutionary analysis of the selected protein

100-ET Coverage : Importance of each residue in the selected protein. Higher the value (warmer the color) the more important.

EA (Most Frequent Variant) : Evolutionary Action of the most frequent variant at each amino acid position in the current SARS-CoV-2 outbreak.

Higher EA value suggests more functional impact of that substitution

Unique Variants : number of unique amino acid substitution at each position.

All Variants : number of total amino acid substitution at each position.

Amino Acid Position

Selecting the residues for structure viewer

Zoom in to regions of interest by dragging a box over the bar plots or using the residue number input box.

Click “add sequence to structure” to add a selection to the Structure Viewer, which can be highlighted in the protein structure.

Residue Start:

Residue End:

Residue length:

Visualization of the evolutionary analysis results on the protein structure. Protein structure is preload with ET color. To focus on a specific region, use the EA/ET Viewer to select regions of interest then drag to the display box. Check Structure Options to map EA, Unique Variants, and All Variants to the structure. Linear and structural epitopes are defined as connected amino acids (linear or spatial) with ET coverage < 30 and not mutated in the current outbreak. They can be selected through the epitope boxes

All selected sequence ranges

Reset all selection

Drag and drop the ranges onto structure

Reset structure

ET on structure

The Evolutionary Action (EA) distribution of all variants and unique variants observed in the current outbreak of the selected protein. Higher EA suggest more functional impact for a give substitution. A protein with EA distribution shifting towards higher values suggest it is likely under selection

All Variants

Unique Variants

The EA scores for all possible mutations for the selected protein

*Purple - predicted more neutral mutation

*Red - predicted more deleterious mutation

Selected protein was blasted against Uniref90, Uniref100 and NCBI nr for homology. Sequences that pass our filter were used to run evolutionary analysis.







Files available for download:

Data version: December 2020

All data files(Includes PyMOL file for selected structure) All data zip file
ET ranks file protein.ranks
EA predicted score protein.pred
nr Treefile protein.nr.nhx
u90 Treefile protein.u90.nhx
u100 Treefile protein.u100.nhx
nr Alignment file alignment.nr.fa
u90 Alignment file alignment.u90.fa
u100 Alignment file alignment.u100.fa
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