ViruSurf

an integrated database to investigate viral sequences

authored by

Arif Canakoglu, Pietro Pinoli, Anna Bernasconi, Tommaso Alfonsi, Damianos p Melidis, Stefano Ceri

Abstract

ViruSurf, available at gmql.eu/virusurf/, is a large public database of viral sequences and integrated and curated metadata from heterogeneous sources (RefSeq, GenBank, COG-UK and NMDC); it also exposes computed nucleotide and amino acid variants, called from original sequences. A GISAID-specific ViruSurf database, available at gmql.eu/virusurf gisaid/, offers a subset of these functionalities. Given the current pandemic outbreak, SARS-CoV-2 data are collected from the four sources; but ViruSurf contains other virus species harmful to humans, including SARS-CoV, MERS-CoV, Ebola and Dengue. The database is centered on sequences, described from their biological, technological and organizational dimensions. In addition, the analytical dimension characterizes the sequence in terms of its annotations and variants. The web interface enables expressing complex search queries in a simple way; arbitrary search queries can freely combine conditions on attributes from the four dimensions, extracting the resulting sequences. Several example queries on the database confirm and possibly improve results from recent research papers; results can be recomputed over time and upon selected populations. Effective search over large and curated sequence data may enable faster responses to future threats that could arise from new viruses.

Organisation(s)

L3S Research Centre

External Organisation(s)

Politecnico di Milano

Type

Article

Journal

Nucleic Acids Research

Volume

49

Pages

D817-D824

ISSN

0301-5610

Publication date

08.01.2021

Publication status

Published

Peer reviewed

Yes

ASJC Scopus subject areas

Genetics

Sustainable Development Goals

SDG 3 - Good Health and Well-being

Electronic version(s)

https://doi.org/10.1093/nar/gkaa846 (Access: Open)