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

William Speier, Michael F. Ochs

Research output: Contribution to journalArticlepeer-review

Abstract

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.

Original languageEnglish (US)
Pages (from-to)2858-2859
Number of pages2
JournalBioinformatics
Volume28
Issue number21
DOIs
StatePublished - Nov 2012

ASJC Scopus subject areas

  • Biochemistry
  • Molecular Biology
  • Computational Theory and Mathematics
  • Computer Science Applications
  • Computational Mathematics
  • Statistics and Probability
  • Medicine(all)

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