Skip to main page content
U.S. flag

An official website of the United States government

Dot gov

The .gov means it’s official.
Federal government websites often end in .gov or .mil. Before sharing sensitive information, make sure you’re on a federal government site.

Https

The site is secure.
The https:// ensures that you are connecting to the official website and that any information you provide is encrypted and transmitted securely.

Access keys NCBI Homepage MyNCBI Homepage Main Content Main Navigation
. 2008 Jan;36(Database issue):D539-42.
doi: 10.1093/nar/gkm951. Epub 2007 Nov 4.

VFDB 2008 release: an enhanced web-based resource for comparative pathogenomics

Jian Yang  1 , Lihong Chen, Lilian Sun, Jun Yu, Qi Jin
Affiliations

VFDB 2008 release: an enhanced web-based resource for comparative pathogenomics

Jian Yang et al. Nucleic Acids Res. 2008 Jan.

Abstract

Virulence factor database (VFDB) was set up in 2004 dedicated for providing current knowledge of virulence factors (VFs) from various medical significant bacterial pathogens to facilitate pathogenomic research. Nowadays, complete genome sequences of almost all the major pathogenic microbes have been determined, which makes comparative genomics a powerful approach for uncovering novel virulence determinants and hidden aspects of pathogenesis. VFDB was therefore upgraded to present the enormous diversity of bacterial genomes in terms of virulence genes and their organization. The VFDB 2008 release includes the following new features; (i) detailed tabular comparison of virulence composition of a given genome with other genomes of the same genus, (ii) multiple alignments and statistical analysis of homologous VFs and (iii) graphical comparison of genomic organizations of virulence genes. Comparative analysis of the numerous VFs will improve our understanding of the nature and evolution of virulence, as well as the development of new therapeutic and preventive strategies. VFDB 2008 release offers more user-friendly tools for comparative pathogenomics and it is publicly accessible at http://www.mgc.ac.cn/VFs/.

PubMed Disclaimer

Figures

Figure 1.
Figure 1.
Comparative pathogenomic results of four sequenced Listeria genomes. (A) Full tabular comparison of pathogenomic composition. (B) Graphical overview for the comparison of pathogenomic organization. VF genes are color-coded by their functional classifications. Homologues between each adjacent pair of genomes are indicated by connecting lines for convenience of further interpretation.
See this image and copyright information in PMC

References

    1. Becker K, Hu Y, Biller-Andorno N. Infectious diseases- a global challenge. Int. J. Med. Microbiol. 2006;296:179–185. - PMC - PubMed
    1. Chen L, Yang J, Yu J, Yao Z, Sun L, Shen Y, Jin Q. VFDB: a reference database for bacterial virulence factors. Nucleic Acids Res. 2005;33:D325–D328. - PMC - PubMed
    1. Pruitt KD, Tatusova T, Maglott DR. NCBI reference sequences (RefSeq): a curated non-redundant sequence database of genomes, transcripts and proteins. Nucleic Acids Res. 2007;35:D61–D65. - PMC - PubMed
    1. Altschul SF, Madden TL, Schaffer AA, Zhang J, Zhang Z, Miller W, Lipman DJ. Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res. 1997;25:3389–3402. - PMC - PubMed
    1. Yang J, Chen L, Yu J, Sun L, Jin Q. ShiBASE: an integrated database for comparative genomics of Shigella. Nucleic Acids Res. 2006;34:D398–D401. - PMC - PubMed

Publication types

Substances