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. 2015 Jan;43(Database issue):D571-7.
doi: 10.1093/nar/gku1207. Epub 2014 Nov 26.

NCBI viral genomes resource

J Rodney Brister  1 , Danso Ako-Adjei  2 , Yiming Bao  2 , Olga Blinkova  2
Affiliations

NCBI viral genomes resource

J Rodney Brister et al. Nucleic Acids Res. 2015 Jan.

Abstract

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.

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Figures

Figure 1.
Figure 1.
Number of validated virus and viroid segments. The numbers of validated virus and viroid segments available in INSDC databases are depicted by the black line, and the numbers of RefSeq virus and viroid segments by the gray columns. Data was calculated at the end of each year from 2000 to 2014, except for 2014 when data was calculated on September 15. INSDC influenza virus segments are not included.
Figure 2.
Figure 2.
Number of ICTV species and viral RefSeq genomes. The numbers of viral species in the NCBI Taxonomy database that are represented by a RefSeq genome record are depicted by the gray bars, and the number of viral species recognized by the ICTV by the black area. Data was calculated at the end of each year from 2000 to 2014, except for 2014 when data was calculated on September 15. The number of ICTV recognized viral species for each year shown was derived from http://www.ictvonline.org/taxonomyReleases.asp.
Figure 3.
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.
See this image and copyright information in PMC

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