GDHDF5 - A Genetic Diversity Database Server

With the advancement of cheap sequencing and genotyping platforms, the personal genomics is moving closer from a promise to a reality in the biomedical research, and genomic selection could become a common practice in plant and animal breeding within a decade. One of the computational challenges is the development of an efficient database system that can deliver fast query access of a table with trillions of data points. Traditionally, most of the biological database system are implemented on SQL based RDBMS, e.g. the new variation module in the Ensembl database. We have developed a genetic diversity database server accessible via network sockets and using Hierarchical Data Format v.5 (HDF5) as the data storage medium. The server is written in C and uses native HDF5 API interface to carry out very fast and efficient data search, export and import. The server uses a custom set of database commands tailored to the genetic diversity queries and allows for account-based data access control. We also provide a Perl module as an interface to the server, which can be used to incorporate GDHDF5 server queries into bioinformatics pipelines. A Perl based ASP website is also provided, enabling graphical interface access to GDHDF5 data for general users.