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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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Related in: MedlinePlus

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.
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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.

Mentions: There are now 71 628 validated viral and viroid genome segments deposited within INSDC databases, not including influenza sequences, which are stored in a specialized database (11,25). This figure represents a nearly 9-fold increase since 2000 (Figure 1), and this rise reflects both steady increases in the number of novel viruses sequenced—as measured by the number of RefSeq genome segments—and a large increase in the number of genome neighbors, i.e. genome sequences belonging to viral species already represented by a RefSeq (Figure 1). As shown in Table 1, RefSeq genome segments are distributed among all viruses, but genome neighbor segments are concentrated among smaller, ssDNA, RNA, and retro-transcribing viruses. Although many of these neighbor genomes are concentrated among human pathogens, there are also several viruses of agricultural importance with high numbers of sequenced genomes (Table 2). While most of the viruses in Table 2 are well studied in the laboratory, many other sequenced viruses are not.


NCBI viral genomes resource.

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

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.
© Copyright Policy
Related In: Results  -  Collection

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

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.
Mentions: There are now 71 628 validated viral and viroid genome segments deposited within INSDC databases, not including influenza sequences, which are stored in a specialized database (11,25). This figure represents a nearly 9-fold increase since 2000 (Figure 1), and this rise reflects both steady increases in the number of novel viruses sequenced—as measured by the number of RefSeq genome segments—and a large increase in the number of genome neighbors, i.e. genome sequences belonging to viral species already represented by a RefSeq (Figure 1). As shown in Table 1, RefSeq genome segments are distributed among all viruses, but genome neighbor segments are concentrated among smaller, ssDNA, RNA, and retro-transcribing viruses. Although many of these neighbor genomes are concentrated among human pathogens, there are also several viruses of agricultural importance with high numbers of sequenced genomes (Table 2). While most of the viruses in Table 2 are well studied in the laboratory, many other sequenced viruses are not.

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