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

82. The Genome Database -- Integrating Maps with Sequence

Christopher J. Porter, C. Conover Talbot Jr., and A. Jamie Cuticchia

The Johns Hopkins University, Baltimore, MD and The Hospital for Sick Children, Toronto, ON, Canada

jamie@bioinfo.sickkids.on.ca

As reported at the 1999 Contractor-Grantee Workshop, the Genome Database (GDB) is now hosted by the Bioinformatics Supercomputing Centre (BiSC) of the Hospital for Sick Children, Toronto. The database was transferred in May 1999, and has since been moved to an SP supercomputer, donated to the GDB project by IBM.

GDB introduced a number of new tools during 1999. We have used NCBI's electronic PCR (e-PCR) software in a tool that retrieves GDB Amplimers predicted to amplify from a sequence. GDB-BLAST uses the BLAST server on BiSC's Origin supercomputer, and displays GDB objects linked to the sequences retrieved. Additionally, output from BiSC's public high speed BLAST server was modified to display links to GDB. BiSC's supercomputers made feasible the use of e-PCR to create a database of potential amplification sites for GDB Amplimers in all public human sequence.

These resources are serving to improve GDB's mapping of Amplimers and Genes. Work progresses to integrate the extensive body of variation and SNP data from GDB into sequence-level maps.

The recent release of a full sequence of chromosome 22 has served as a proving ground for the integration of GDB data with the complete human sequence. BiSC's sequence analysis tools were used to map GDB objects onto the sequence. These results are displayed as a interactive graphical map, and are being integrated into GDB's comprehensive map. These approaches show how GDB will integrate classical mapping information with the rapidly emerging genomic sequence.

Collaborations with sequencing centers and the Genome Annotation Consortium are continuing to load clone tiling paths into GDB, and to create bidirectional links between GDB records and the annotated sequence.

International interest in GDB continues - 1999 saw the establishment of a new GDB node in Beijing, China, and work is underway to create a node in Bangalore, India.