NCBI Viral Genomes Resource

By J. R. Brister, Danso Ako-Adjei, Yīmíng Bào, O. Blinkova. Nucleic Acids Res., 2014

599 citations recorded by the source corpus.

Recent technological innovations have ignited an explosion in virus genome sequencing that promises to fundamentally alter our understanding of viral biology and profoundly impact public health policy. Yet, any potential benefits from the billowing cloud of next generation sequence data hinge upon well implemented reference resources that facilitate the identification of sequences, aid in the assembly of sequence reads and provide reference annotation sources. The NCBI Viral Genomes Resource is a reference resource designed to bring order to this sequence shockwave and improve usability of viral sequence data. The resource can be accessed at http://www.ncbi.nlm.nih.gov/genome/viruses/ and catalogs all publicly available virus genome sequences and curates reference genome sequences. As the number of genome sequences has grown, so too have the difficulties in annotating and maintaining reference sequences. The rapid expansion of the viral sequence universe has forced a recalibration of the data model to better provide extant sequence representation and enhanced reference sequence products to serve the needs of the various viral communities. This, in turn, has placed increased emphasis on leveraging the knowledge of individual scientific communities to identify important viral sequences and develop well annotated reference virus genome sets.

Subfields: Animal Science and Zoology, Ecology, Plant Science

View Paper: https://www.semanticscholar.org/paper/5d411b726b52597f43d5f7a3568e092165ceee10

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In Animal Science and Zoology

Eugene V. Koonin

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In Plant Science

Citations in the corpus

Database resources of the National Center for Biotechnology Information. (2019, methodology): “This resource includes data from our Viral Genomes Resource (13) and is available now for use by the public.”
A review of methods and databases for metagenomic classification and assembly (2019, background): “gov/genome/viruses/) [156] provides links to other validated viral genomes that are ‘neighbors’ (i.”
BUSCO Update: Novel and Streamlined Workflows along with Broader and Deeper Phylogenetic Coverage for Scoring of Eukaryotic, Prokaryotic, and Viral Genomes (2021, methodology): “Supplementary figure 5 and supplementary table 6, Supplementary Material online, show the assessment on RefSeq (Brister et al. 2015) viral genomes and gene sets using the “–auto-lineage” function.”
NCBI Taxonomy: a comprehensive update on curation, resources and tools (2020, background): “Now,however, complete or nearly complete phage genomes are classified according to phylogenies provided by the NCBI RefSeq virus group that is responsible for resources dedicated to virus information (78, 79).”
Prokaryotic Virus Orthologous Groups (pVOGs): a resource for comparative genomics and protein family annotation (2016, background): “Despite the presence of many thousands of completely sequenced virus genomes in NCBI sequence databases, the vast majority of viruses still remain to be characterized (3).”
Virus Variation Resource – improved response to emergent viral outbreaks (2016, background): “The nucleotide and protein sequences within these records can be invaluable for the unambiguous assignment of sequences to defined groups and can also serve as repositories of reference sequence feature annotation maintained by in-house curation efforts often in collaboration with other scientists (”
KrakenUniq: confident and fast metagenomics classification using unique k-mer counts (2018, background): “Furthermore, KrakenUniq implements additional new features to improve metagenomics classification: (a) searches can be done against multiple databases hierarchically; (b) the taxonomy can be extended to include nodes for strains and plasmids, thus enabling their detection; and (c) the database build”
Reference sequence (RefSeq) database at NCBI: current status, taxonomic expansion, and functional annotation (2015, methodology): “Additional genomes for a given species are validated for taxonomy and completeness and then indexed as sequence ‘neighbors’ (52).”
Database resources of the National Center for Biotechnology Information (2014, methodology): “The repository can capture fully annotated raw and processed data, enabling compliance with reporting standards such as ‘Minimum Information About a Microarray Experiment’ (MIAME) (23,24).”