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Bioinformatics Advance Access originally published online on September 6, 2008
Bioinformatics 2008 24(21):2564-2565; doi:10.1093/bioinformatics/btn477
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© 2008 The Author(s)
This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/2.0/uk/) which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.

varDB: a pathogen-specific sequence database of protein families involved in antigenic variation

C. Nelson Hayes 1, Diego Diez 1, Nicolas Joannin 2,3, Wataru Honda 1, Minoru Kanehisa 1, Mats Wahlgren 2,3, Craig E. Wheelock 1,2,4,* and Susumu Goto 1,*

1Bioinformatics Center, Institute for Chemical Research, Kyoto University, Uji, Kyoto 611-0011, Japan, 2Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Box 280, SE-17177 Stockholm, 3Swedish Institute for Infectious Disease Control (SMI), SE-17182 Stockholm and 4 Division of Physiological Chemistry II, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, SE-17177 Stockholm, Sweden

*To whom correspondence should be addressed.


  Abstract

Summary: Infectious diseases are a major threat to global public health and prosperity. The causative agents consist of a suite of pathogens, ranging from bacteria to viruses, including fungi, helminthes and protozoa. Although these organisms are extremely varied in their biological structure and interactions with the host, they share similar methods of evading the host immune system. Antigenic variation and drift are mechanisms by which pathogens change their exposed epitopes while maintaining protein function. Accordingly, these traits enable pathogens to establish chronic infections in the host. The varDB database was developed to serve as a central repository of protein and nucleotide sequences as well as associated features (e.g. field isolate data, clinical parameters, etc.) involved in antigenic variation. The data currently contained in varDB were mined from GenBank as well as multiple specialized data repositories (e.g. PlasmoDB, GiardiaDB). Family members and ortholog groups were identified using a hierarchical search strategy, including literature/author-based searches and HMM profiles. Included in the current release are>29 000 sequences from 39 gene families from 25 different pathogens. This resource will enable researchers to compare antigenic variation within and across taxa with the goal of identifying common mechanisms of pathogenicity to assist in the fight against a range of devastating diseases.

Availability: varDB is freely accessible at http://www.vardb.org/

Contact: nelson{at}kuicr.kyoto-u.ac.jp; goto{at}kuicr.kyoto-u.ac.jp

Supplementary information: Supplementary data are available at Bioinformatics online.

Associate Editor: Alfonso Valencia

Received on July 18, 2008; revised on August 28, 2008; accepted on September 4, 2008

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