Updating annotations with the distributed annotation system and the automated sequence annotation pipeline

Abstract

Summary: The integration between BioDAS ProServer and Automated Sequence Annotation Pipeline (ASAP) provides an interface for querying diverse annotation sources, chaining and linking results, and standardizing the output using the Distributed Annotation System (DAS) protocol. This interface allows pipeline plans in ASAP to be integrated into any system using HTTP and also allows the information returned by ASAP to be included in the DAS registry for use in any DAS-aware system. Three example implementations have been developed: the first accesses TRANSFAC information to automatically create gene sets for the Coordinated Gene Activity in Pattern Sets (CoGAPS) algorithm; the second integrates annotations from multiple array platforms and provides unified annotations in an R environment; and the third wraps the UniProt database for integration with the SPICE DAS client.

Availability: Source code for ASAP 2.7 and the DAS 1.6 interface is available under the GNU public license. Proserver 2.20 is free software available from SourceForge. Scripts for installation and configuration on Linux are provided at our website: http://www.rits.onc.jhmi.edu/dbb/custom/A6/

Fig. 1.

A schematic representation of ASAP and DAS integration. The user sends an HTTP request to the ProServer daemon, which is then relayed to the ASAP manager where a job is created. When the job is complete, the results are formatted in XML according to the DAS protocol and returned through the ProServer daemon. Additionally, ASAP sends email notifications and saves the results on the server to be accessed later via the web interface