title: Updating annotations with the distributed annotation system and the automated sequence annotation pipeline.
abstract: CONCLUSIONS
  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.
  
  
  BACKGROUND
  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/
authors.affiliation: Medical Imaging Informatics Group, University of California, Los Angeles, CA, USA. Speier@mii.ucla.edu
authors.forename: William
authors.initials: W
authors.lastname: Speier
authors.forename: Michael F
authors.initials: MF
authors.lastname: Ochs
mesh_terms: D000465:Algorithms; D019295:Computational Biology / Q000379:methods; D016208:Databases, Factual; D059014:High-Throughput Nucleotide Sequencing; D016247:Information Storage and Retrieval / Q000379:methods*; D051188:Knowledge Bases; D058977:Molecular Sequence Annotation / Q000379:methods*; D011381:Programming Languages; D011506:Proteins / Q000737:chemistry; D012984:Software; D014584:User-Computer Interface
chemical_list: D011506:Proteins