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ready ViruSurf

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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 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.




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Publication for citation  ViruSurf: an integrated database to investigate viral sequences. Canakoglu A,Pinoli P,Bernasconi A,Alfonsi T,Melidis DP,Ceri S; Nucleic Acids Res ; 2020; gkaa846;


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Record added: Sept. 18, 2020, 12:41 p.m.
Record updated: Oct. 26, 2020, 9:27 a.m. by acanak.

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ViruSurf: an integrated database to investigate viral sequences.

Canakoglu A,Pinoli P,Bernasconi A,Alfonsi T,Melidis DP,Ceri S
Nucleic Acids Res 2020

View Paper (PubMed) View Publication

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