ViruSurf: An integrated database to investigate viral sequences

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Canakoglu, A.; Pinoli, P.; Bernasconi, A.; Alfonsi, T.; Melidis, D.P. et al.: ViruSurf: An integrated database to investigate viral sequences. In: Nucleic Acids Research 49 (2021), Nr. D1, S. D817-D824. DOI: https://doi.org/10.1093/nar/gkaa846

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To cite the version in the repository, please use this identifier: https://doi.org/10.15488/15729

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Sum total of downloads: 21




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ViruSurf, available at http://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 http://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.
License of this version: CC BY 4.0 Unported
Document Type: Article
Publishing status: publishedVersion
Issue Date: 2020
Appears in Collections:Forschungszentren

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pos. country downloads
total perc.
1 image of flag of United States United States 9 42.86%
2 image of flag of Germany Germany 4 19.05%
3 image of flag of United Kingdom United Kingdom 3 14.29%
4 image of flag of No geo information available No geo information available 2 9.52%
5 image of flag of Japan Japan 2 9.52%
6 image of flag of Iran, Islamic Republic of Iran, Islamic Republic of 1 4.76%

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