MyDas, an extensible Java DAS server

Extension to distributed annotation system: Summary and summaryplot commands

In recent years, the development of high-throughput sequencing technologies provided an effective way to generate data from entire genomes and test variants from thousands of individuals. The information acquired from analysing the data generated from high-throughput sequencing technologies provided useful insights into applications like whole-exome sequencing and targeted sequencing to discover the genetic cause of complex diseases and drug responses. The Distributed Annotation System (DAS) is one of the proposed solution developed to share and unify biological data from multiple local and remote DAS annotation servers. The researchers can use DAS to request data from federated or centralised databases and integrate them into a unified view. Furthermore, with the use of Reference DAS servers, structural and sequence data can be used to accompany annotation data, for the pursue of new knowledge for a particular feature or region. In this paper, two additional commands, summary and summary-plot commands, to the existing DAS protocol are proposed and implemented. The proposed commands were created in order to give the users the capabilities to request a summary of features for a particular region of interest. The summary command was created in order to extend the capabilities of the current DAS protocol, while the summaryplot command was created to provide a more user-friendly alternative to standard XML DAS responses. Finally, three examples are presented based on the GENCODE annotation data.