Database Commons

a catalog of worldwide biological databases

Antigenic variation is a common mechanism employed by many pathogenic organisms to avoid recognition of surface proteins by the host immune system. The malaria parasite, Plasmodium falciparum, among many others, exploits this mechanism and manages to survive in an otherwise hostile environment. Although similarities in the mechanisms used among different species to generate antigenic variation are broadly recognized, there is a lack of studies using cross-species data. The varDB project (http://www.vardb.org) was created to study antigenic variation at a range of different levels, both within and among species. The project aims to serve as a resource to increase our understanding of antigenic variation by providing a framework for comparative studies. In this review we describe the varDB project, its construction, and the overall organization of information with the intent of increasing the utility of varDB to the research community. The current version of varDB supports 27 species involved in 19 different diseases affecting humans as well as other species. These data include 42 gene families that are represented by over 67,000 sequences. The varDB project is still in its infancy but is expected to continue to grow with the addition of new organisms and gene families as well as input from the general research community.

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>29,00 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/