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ViruSurf: an integrated database to investigate viral sequences
Arif Canakoglu1, Pietro Pinoli1, Anna Bernasconi1
1Dipartimento di Elettronica, Informazione e Bioingegneria, Politecnico di Milano, Via Ponzio 34/5, 20133 Milano, Italy.
Nucleic Acids Research
|October 12, 2020
Summary
ViruSurf is a public database offering viral sequences and metadata. It enables complex searches for rapid analysis and response to viral threats like SARS-CoV-2.
Area of Science:
- Bioinformatics
- Virology
- Genomics
Background:
- Viral sequence data is fragmented across multiple sources, hindering comprehensive analysis.
- The need for integrated, curated viral sequence databases is critical for public health surveillance.
- Existing databases may lack advanced search functionalities for complex queries.
Purpose of the Study:
- To introduce ViruSurf, a comprehensive database of viral sequences and metadata.
- To provide a powerful web interface for complex querying of viral genomic and analytical data.
- To support rapid analysis of viral threats, including SARS-CoV-2.
Main Methods:
- Integration and curation of viral sequence data from RefSeq, GenBank, COG-UK, and NMDC.
- Computation and inclusion of nucleotide and amino acid variants.
- Development of a web interface supporting complex, multi-dimensional search queries.
- Inclusion of data for various human pathogens like SARS-CoV-2, MERS-CoV, Ebola, and Dengue.
Main Results:
- ViruSurf provides access to integrated viral sequences and metadata, including computed variants.
- The database supports complex queries combining biological, technological, organizational, and analytical dimensions.
- Example queries demonstrate the potential to confirm and improve upon existing research findings.
- A GISAID-specific ViruSurf database offers a subset of functionalities for SARS-CoV-2 data.
Conclusions:
- ViruSurf offers a valuable resource for researchers and public health officials.
- Effective search capabilities over curated viral sequence data can accelerate responses to emerging viral threats.
- The database facilitates deeper understanding of viral evolution and characteristics.
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