%0 Journal Article %1 canakoglu2021virusurf %A Canakoglu, Arif %A Pinoli, Pietro %A Bernasconi, Anna %A Alfonsi, Tommaso %A Melidis, Damianos P %A Ceri, Stefano %D 2021 %I Oxford University Press %J Nucleic acids research %K bioinformatics database myown sarscov2 viralgenomes %N D1 %P D817--D824 %R 10.1093/nar/gkaa846 %T ViruSurf: an integrated database to investigate viral sequences %U https://academic.oup.com/nar/article/49/D1/D817/5921283?login=true %V 49 %X 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.

@article{canakoglu2021virusurf, abstract = {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.}, added-at = {2021-03-03T09:49:23.000+0100}, author = {Canakoglu, Arif and Pinoli, Pietro and Bernasconi, Anna and Alfonsi, Tommaso and Melidis, Damianos P and Ceri, Stefano}, biburl = {https://www.bibsonomy.org/bibtex/227ea50a7c1964078ddfe6df44b5e1bf2/damianosmel}, description = {This is work stems out from the database group of Prof. Stefano Ceri in the engineering school of Milano. The aim was to contribute on research for SARS-CoV-2 and in viruses in general. This work was conducted during the first pandemic of SARS-CoV-2. To contribute on their idea, I developed Python software to perform MSA (multiple sequence alignment) and to extract homology-based immunodominant regions for structural proteins of Sars-Cov-2 and epitope information for viral genomes in general. }, doi = {10.1093/nar/gkaa846}, interhash = {808dd865472f843c6d061e161f6cadcd}, intrahash = {27ea50a7c1964078ddfe6df44b5e1bf2}, journal = {Nucleic acids research}, keywords = {bioinformatics database myown sarscov2 viralgenomes}, language = {English}, month = {October}, number = {D1}, pages = {D817--D824}, publisher = {Oxford University Press}, timestamp = {2021-03-03T09:49:23.000+0100}, title = {ViruSurf: an integrated database to investigate viral sequences}, url = {https://academic.oup.com/nar/article/49/D1/D817/5921283?login=true}, volume = 49, year = 2021 }