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Fig. 1 | BMC Bioinformatics

Fig. 1

From: CoeViz: a web-based tool for coevolution analysis of protein residues

Fig. 1

A flowchart of CoeViz. Protein data are submitted as defined in the POLYVIEW-2D server ([28], http://polyview.cchmc.org/polyview_doc.html), which includes PDB-formatted coordinate files, output from the sequence-based prediction servers, or custom sequence profiles. At the protein visualization page, there is an option provided to request analysis of covariance of amino acids (CoeViz). The user can choose a covariance metric and a database to generate the MSA or provide a file with the constructed MSA. CoeViz computes a requested covariance or conservation metric with all implemented adjustments separately and performs hierarchical clustering. Once calculations are completed, CoeViz provides an interactive web-interface to review covariance data using heatmaps, circular diagrams, and clustering trees. From the circular diagrams, the user has options to map identified correlated amino acids to a protein 3D structure or sequence depending on the input data. All generated results can be exported in text or graphics formats

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