Genome Informatics Section 

DOE Human Genome Program Contractor-Grantee Workshop VII 
January 12-16, 1999  Oakland, CA
79. Visualization, Navigation, and Query of Genomes: The Genome Channel and Beyond 

Morey Parang, Richard Mural, Manesh Shah, Doug Hyatt, Miriam Land, Jay Snoddy, Edward C. Uberbacher, and the Genome Annotation Consortium 
Computational Biosciences Section, Life Sciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 
ube@ornl.gov 
http://compbio.ornl.gov/gac 

We are developing and deploying a series of interface tools for visualizing and querying the reference human genome and other genomes assembled and annotated by the Genome Annotation Consortium (see related abstracts). The Genome Channel Browser is a Java 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 provides a diverse set of functional features in a DNA sequence including PolyA sites, CpG islands, repetitive DNA, simple repeats, STSs, GRAIL2 and Genscan exons, as well as GRAIL-EXP and Genscan gene models and their respective protein translations. The underlying information and evidence for genes and other features is presented in a variety of text windows, graphics windows, and summary reports. 

The new version of the Genome Channel Browser (v2.0) offers such improved user interface and additional capabilities as the following: 

  • 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.
  • Pattern searches against genomes that return genome location and context of related sequences (Visual Genome Search Server).
In addition to Java-based browsing, several HTML-based interfaces to Genome Channel data are being developed. Genome, chromosome, contig, and clone summary reports, gene and protein lists, homologies, and other features are available for browsing and querying. For example, the chromosome summary report includes the following for each chromosome: (1) the acquired genomic sequences (including clones from GenBank/NCBI/DDBJ and genome centers); (2) the assembled sequences (number of contigs, nucleotide length of assembled contigs, and estimated percent completion of contiguous sequence for each chromosome); and (3) genes (including number of GenBank human annotated genes, Genscan predicted genes, total GRAIL-EXP genes, and those that have at least partial EST evidence); and other features. Browsable and queryable lists of genes, their protein translations, and homologs are compiled with links to related information in multiple databases. Compilations of other features, including STS sequences that are attached to genome sequence contigs, link the genomic sequence to genetic and RH maps. 

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 polymorphisms and mutations. 

 
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