Journal Article

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

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

in Bioinformatics

Volume 24, issue 21, pages 2564-2565
Published in print November 2008 | ISSN: 1367-4803
Published online September 2008 | e-ISSN: 1460-2059 | DOI: http://dx.doi.org/10.1093/bioinformatics/btn477

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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@kuicr.kyoto-u.ac.jp; goto@kuicr.kyoto-u.ac.jp

Supplementary information: Supplementary data are available at Bioinformatics online.

Journal Article.  996 words. 

Subjects: Bioinformatics and Computational Biology

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