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NCBI viral genomes resource.

Brister JR, Ako-Adjei D, Bao Y, Blinkova O - Nucleic Acids Res. (2014)

Bottom Line: 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 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.

View Article: PubMed Central - PubMed

Affiliation: National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA jamesbr@ncbi.nlm.nih.gov.

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Distribution of host types among viral RefSeq genomes. The distribution of viral host types assigned to RefSeq genomes is depicted for algae, archaea, bacteria, environment, fungi, human, invertebrates, plants, protozoa and vertebrates host groups. Diatom is not shown.
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Figure 3: Distribution of host types among viral RefSeq genomes. The distribution of viral host types assigned to RefSeq genomes is depicted for algae, archaea, bacteria, environment, fungi, human, invertebrates, plants, protozoa and vertebrates host groups. Diatom is not shown.

Mentions: The second model captures and standardizes host information for all viruses, and whenever a new RefSeq record is created, a manually curated ‘viral host’ property is assigned to the relevant species within the NCBI Taxonomy database. The property defines higher order, biologically relevant taxonomic host groups—algae, archaea, bacteria, diatom, environment, fungi, human, invertebrates, plants, protozoa and vertebrates—and enable sorting and selection of sequences within the NCBI Taxonomy (http://www.ncbi.nlm.nih.gov/taxonomy) and Viral Genomes Resource. For example searching the NCBI Taxonomy database with the term ‘vhost fungi’[Properties] (quotes included) will return a list of taxonomy groups comprised of viruses that infect fungi. Users can then select the ‘Genome’ database from ‘Find related data’ link on the Taxonomy search page to view all viral genomes associated with viruses retrieved from the search. In cases where a virus infects multiple types of organisms, multiple terms are assigned, for example ‘invertebrates, plants’. To search NCBI Taxonomy for viruses that infect multiple hosts simply include ‘AND’ between search terms, for example ‘vhost invertebrates’[Properties] AND ‘vhost plants’[Properties] (quotes included). The current distribution of assigned viral host terms is shown in Figure 3.


NCBI viral genomes resource.

Brister JR, Ako-Adjei D, Bao Y, Blinkova O - Nucleic Acids Res. (2014)

Distribution of host types among viral RefSeq genomes. The distribution of viral host types assigned to RefSeq genomes is depicted for algae, archaea, bacteria, environment, fungi, human, invertebrates, plants, protozoa and vertebrates host groups. Diatom is not shown.
© Copyright Policy
Related In: Results  -  Collection

Show All Figures
getmorefigures.php?uid=PMC4383986&req=5

Figure 3: Distribution of host types among viral RefSeq genomes. The distribution of viral host types assigned to RefSeq genomes is depicted for algae, archaea, bacteria, environment, fungi, human, invertebrates, plants, protozoa and vertebrates host groups. Diatom is not shown.
Mentions: The second model captures and standardizes host information for all viruses, and whenever a new RefSeq record is created, a manually curated ‘viral host’ property is assigned to the relevant species within the NCBI Taxonomy database. The property defines higher order, biologically relevant taxonomic host groups—algae, archaea, bacteria, diatom, environment, fungi, human, invertebrates, plants, protozoa and vertebrates—and enable sorting and selection of sequences within the NCBI Taxonomy (http://www.ncbi.nlm.nih.gov/taxonomy) and Viral Genomes Resource. For example searching the NCBI Taxonomy database with the term ‘vhost fungi’[Properties] (quotes included) will return a list of taxonomy groups comprised of viruses that infect fungi. Users can then select the ‘Genome’ database from ‘Find related data’ link on the Taxonomy search page to view all viral genomes associated with viruses retrieved from the search. In cases where a virus infects multiple types of organisms, multiple terms are assigned, for example ‘invertebrates, plants’. To search NCBI Taxonomy for viruses that infect multiple hosts simply include ‘AND’ between search terms, for example ‘vhost invertebrates’[Properties] AND ‘vhost plants’[Properties] (quotes included). The current distribution of assigned viral host terms is shown in Figure 3.

Bottom Line: 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 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.

View Article: PubMed Central - PubMed

Affiliation: National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA jamesbr@ncbi.nlm.nih.gov.

Show MeSH
Related in: MedlinePlus