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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.

Recent Enhancements to the LLNL Genome Browser: Automated Construction & Display of Physical Maps

Mark Wagner (mwagner@kooler.llnl.gov), Tom Slezak, and Elbert Branscomb
Human Genome Center, L-452, Biology and Biotechnology Research Program, Lawrence Livermore National Laboratory, Livermore, California 94550.

The LLNL Genome Browser has undergone extensive enhancement since the last Workshop in February 1993. Our design seeks to provide access and visual display of all data generated by our Human Genome mapping project free of any prejudgment as to what questions are of interest or what objects, properties, and relationships should be displayed at any time. We use a flexible object-based mechanism to track over 600,000 relationships on over 185,000 potentially-mappable objects on human chromosome 19. Rather than forcing all mapping data into a single picture we use a linked collection of displays, each tuned to the needs of a specific level of detail.

New displays have been developed that enable us to manipulate integrated maps of chromosome 19. The partial order map portion of the browser relates our cosmid clones, some of which are partially ordered via FISH and genetic means, to larger entities (YACs, BACs, PACs, cosmid contigs, and Restriction Fragment maps). Although this map does not take into account distance and length information, a "metric map" module adds this extra and often conflicting data. The first generation assembly algorithms used for this construction utilize an ordered greedy approach to position the objects relative to each other. We will continue to refine and expand our capabilities in this area in the coming year.

Restriction Fragment Maps are also generated and displayed, with fragments containing attributes, such as gene exons, indicated. Well over half of ch19 is now mapped at this level of detail.

Relationships between types of maps are indicated through the use of a display that permits the user to see all possible map types that a selected object appears in, and permits the user to view that object instantly in those other maps. For example, this permits the user to select a cosmid in a contig, note that the same cosmid is in a restriction fragment map, and see that cosmid in the map with a single mouse click. Our current version of the browser is in daily use by over 40 biologists at LLNL and is also being used by our collaborators at ORNL, exploiting the client/server design.

This work was performed under the auspices of the U.S. Department of Energy by Lawrence Livermore National Laboratory contract no. W-7405-ENG-48.