DOE Human Genome Program Contractor-Grantee Workshop VIII
February 27-March 2, 2000  Santa Fe, NM

61. Navigation, Visualization, and Query of Genomes: The Genome Channel and Beyond

Morey Parang, Miriam Land, Denise Schmoyer, Jay Snoddy, Doug Hyatt, Richard Mural, and Ed Uberbacher

Computational Biosciences and Toxicology and Risk Analysis Sections, Life Sciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831

http://compbio.ornl.gov/

The Genome Channel Browser is a Java based viewer capable of representing a wide variety of genomic-sequence annotation and links to a large number of related information and data resources. It relies on a number of underlying data resources, analysis tools, and data-retrieval agents to provide an up-to-date view of genomic sequences as well as computational and experimental annotation. The current version of the Genome Channel Browser (v2.0) provides a diverse set of functional features. New features in this version of the Genome Channel include: additional features such as tRNA and BAC ends, additional organisms including microbes, genetic and radiation hybrid maps, extended and detailed listing of features and generation of summary reports, text-based searches and query of underlying data, BLAST searches against individual or combined assembled sequences and products, and pattern searches against genomes that return genome location and context of related sequences.

In addition to Java-based browsing, the Genome Catalog, an HTML-based interface to the Genome Channel is under development. Genome, chromosome, contig, and clone summary reports, gene and protein lists, homologies, and other features are available for browsing and querying through this interface. We are researching the feasibility of providing interfaces to additional types of analysis results, such as protein threading and structural classification that might provide clues to the functions of predicted genes. Other features being studied for future implementation and visualization include gene expression data, polymorphisms and mutations.

(Research sponsored by the Office of Biological and Environmental Research, USDOE under contract number DE-AC05-96OR22464 with Lockheed Martin Energy Research Corp.)