ViruSurf: an integrated database to investigate viral sequences.
Nucleic Acids Res
; 49(D1): D817-D824, 2021 01 08.
Article
in English
| MEDLINE | ID: covidwho-851820
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.
Full text:
Available
Collection:
International databases
Database:
MEDLINE
Main subject:
Genome, Viral
/
Computational Biology
/
Databases, Genetic
/
Data Curation
/
SARS-CoV-2
/
COVID-19
Type of study:
Observational study
Topics:
Variants
Limits:
Humans
Language:
English
Journal:
Nucleic Acids Res
Year:
2021
Document Type:
Article
Affiliation country:
Nar
Similar
MEDLINE
...
LILACS
LIS