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Welcome to the Wiki Page of EpiViruSurf!
EpiViruSurf is a Web application for selecting viral populations of interest and then analyzing how their amino acid changes are distributed throughout epitopes.
Viral sequences are searched within ViruSurf, which stores curated metadata and amino acid changes imported from the most widely used deposition sources for viral databases (GenBank, COG-UK, and GISAID).
Epitopes are searched within the open-source Immune Epitope Database (IEDB) or directly proposed by users by indicating their start and stop positions in the context of a given viral protein.
Amino acid changes of selected populations are joined with epitopes of interest; a result table summarizes, for each epitope, statistics about the overlapping amino acid changes and about the sequences carrying such alterations. Results may also be inspected by the VirusViz Web application; epitope regions are highlighted within the given viral protein, and changes can be comparatively inspected. For sequences mutated on the epitope, we also offer a complete view of the amino acid changes distribution, optionally grouped by location, collection date, or lineage.
Thanks to its functionalities, EpiViruSurf supports user-friendly testing of epitope conservancy within selected populations of interest, which can be of uttermost relevance for designing vaccines, drugs, or serological assays. See Examples-of-use page to see possible applications.
If you need information on our database and data sources, start here
If you need a rich introduction to the interface, start here
---> If you are impatient... and want a quick introduction with an example, start here! <---
If you wish to see a simple walk-through example and three rich use cases, start here
You should finally read our Disclaimer, What we support, and the External software
We are a group of Bioinformatics researchers from Politecnico di Milano, led by Prof. Stefano Ceri. You can see our Data-driven Genomic Computing Project here The EpiViruSurf project has been led by Dr. Arif Canakoglu and built by the team as indicated here.
Thanks to our previous knowledge in human genomics (documented with our conceptual model focused on human genomics, pipeline for genomic data integration, and database for genomic sequences, searchable through the GenoSurf Web Interface), we have been able to rapidly design corresponding systems for the domain of viral genomics.
In April 2020, we proposed the Viral Conceptual Model (VCM), which was developed by interviewing a variety of experts of the various aspects of virus research (including clinicians, epidemiologists, drug and vaccine developers). In August 2020, we produced the corresponding curated database ViruSurf http://gmql.eu/virusurf/, which integrates viral sequences from NCBI GenBank, RefSeq, COG-UK, NMDC and has a special endpoint for data deposited into GISAID http://gmql.eu/virusurf_gisaid/. In Spring 2021, we are proposing EpiViruSurf http://gmql.eu/epivirusurf/, an instrument that supports user-friendly testing of epitope conservancy within selected populations of interest, which can be of uttermost relevance for designing vaccines, drugs, or serological assays.