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GAIA: framework annotation of genomic sequence

L C Bailey1, S Fischer, J Schug

  • 1Computational Biology and Informatics Laboratory, Department of Genetics, University of Pennsylvania School of Medicine, Philadelphia, Pennsylvania 19104-6021, USA. bailey@www.cbil.upenn.edu

Genome Research
|May 16, 1998
PubMed
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Framework annotation offers high-throughput, reliable DNA sequence analysis for initial biologic characterization. The Genome Annotation and Information Analysis (GAIA) system provides a foundation for laboratory experiments using genomic data.

Area of Science:

  • Genomics
  • Bioinformatics
  • Computational Biology

Background:

  • Genomic sequence data is rapidly increasing, making DNA sequences a primary reagent in biological investigations.
  • The role of annotation in guiding laboratory experiments is expanding.
  • There is a need for efficient and reliable methods for initial characterization of unexamined genomic sequences.

Purpose of the Study:

  • To describe a high-throughput, reliable annotation process called framework annotation.
  • To introduce Genome Annotation and Information Analysis (GAIA), a prototype software architecture for framework annotation.
  • To demonstrate the effectiveness of framework annotation as a starting point for biological investigation.

Main Methods:

  • Developed GAIA, a prototype software architecture centered around an annotation database.

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  • Designed a database schema with three core concepts: Entries (sequence and historical data), Features (biological information), and Experiments (evidence).
  • Utilized CARTA, autonomous sensors, to perform automatic analyses and generate framework annotation.

    • Main Results:

    • GAIA's database allows tracking of annotation results and assessment of reliability.
    • A Web-based query interface with graphical Java applets and HTML pages enables interactive data exploration.
    • Initial application of framework annotation to test sequences demonstrated its effectiveness.

    Conclusions:

    • Framework annotation provides a foundation for initial biological characterization of genomic sequences.
    • The GAIA prototype effectively implements framework annotation principles.
    • The system is available for public use and comment to facilitate further development.