Introduction to the Workshop
URLs Provided by Attendees

Abstracts

Mapping

Informatics

Sequencing

Instrumentation

Ethical, Legal, and Social Issues

Infrastructure

The electronic form of this document may be cited in the following style:
Human Genome Program, U.S. Department of Energy, DOE Human Genome Program Contractor-Grantee Workshop IV, 1994.

Abstracts scanned from text submitted for November 1994 DOE Human Genome Program Contractor-Grantee Workshop. Inaccuracies have not been corrected.

Informatics Support for Mapping in Mouse-Human Homology Regions

Sergey Petrov [1], Manesh Shah [1], Loren Hauser [1], Richard Mural [2], and Edward Uberbacher [1]
Engineering Physics and Mathematics Division [1] and Biology Division [2], Oak Ridge National Laboratory, Oak Ridge, TN 37831-6364
615/574-6134, Fax 615/574-7860, Internet:"UBE@ornl.gov"

The purpose of this project is to develop databases and tools for the ORNL Mouse-Human Mapping Project, including the construction of a mapping database for the project, tools for management and archiving of cDNAs and other probes used in the laboratory, and analysis tools for mapping, inter-specific backcross, and other needs. Our initial effort has involved installing and developing a relational SYBASE database for tracking samples and probes, experimental results, analysis, etc. Recent work has focused on a corresponding ACeDB implementation containing mouse mapping data and which provides numerous graphical views of this data. The initial relational database has been constructed with SYBASE using a schema modeled from the one implemented at the LLNL center because of the available documentation for the LLNL system, and to maximize compatibility with the human chromosome 19 mapping effort (major homologies exist between human chromosome l9 and mouse chromosome 7 - the initial focus of the ORNL work). Our ACeDB implementation has been modeled somewhat from the chromosome 21 ACeDB system at LBL (with some model modification) and is designed to contain genetic and physical mouse map data as well as homologous human chromosome data. The utility of exchanging map information with LLNL (human chromsome 19) and potentially other centers has lead to the implementation of procedures for data export, and import of human mapping data into the ORNL databases.

User access to the system is being provided by workstation forms-based data entry and ACeDB graphical data browsing. We have also implemented the LLNL databases browser to view the human chromosome l9 data maintained at LLNL, and arrangements are being made to incorporate mouse mapping information into the browser. Other applications such as the "Encyclopedia of the Mouse", specific tools for archiving and tracking cDNAs and other mapping probes, and analysis of inter-specific backcross data and restriction mapping of YACs have been implemented.

We would like to acknowledge use of ideas from the LLNL and LBL Human Genome Centers. (Research sponsored by the Office of Health and Environmental Research, U.S. Department of Energy, under contract DE-AC05-84OR21400 with Martin Marietta Energy Systems, Inc.)