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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.

SIGMA: System for Integrated Genome Map Assembly

Michael J. Cinkosky, Shahar Tsadeek, and James W. Fickett
National Center for Genome Resources
1800 Old Pecos Trail
Santa Fe, NM 87505
(505) 982-7840

SIGMA (System for Integrated Genome Map Assembly) is an interactive, graphical genome map editor. SIGMA enables maps to be built from many different types of mapping data including: YAC/STS content, genetic linkage, breakpoint, in situ hybridization, radiation hybrid, etc. All of the data are integrated into a single map and SIGMA is able to identify discrepancies between the map and the data on which it is based.

SIGMA has the following major features:

• Graphical, mouse-based genome map editing;
• Supports creation of multiple, user-defined "views" on a single map;
• Enables integration of data at all appropriate levels of resolution, from banded ideograms to restriction fragments;
• Allows users to add new kinds of cloning vectors, chromosome landmarks, or other map objects, without changing the software;
• Split screen allows simultaneous viewing of maps at multiple levels of magnification;
• Able to print maps of any size on any PostScript(tm) printer;
• Supports integration of data from many different types of physical and linkage experiments;
• Keeps the underlying data as part of the map, allowing users to easily access the data supporting any given map;
• Automatically evaluates the map against the underlying data, pointing out places where the two disagree;
• Available for multiple platforms, including:
  

  Sun SparcStation, under Sun/OS 4.X
  

  Apple Macintosh
  

  DEC Alpha, underOSF-1
  

SIGMA is currently being used to assemble maps of a number of human chromosomes, including 5, 9, 16, X and Y.

SIGMA is available by anonymous ftp from ftp.ncgr.org. Documentation on the software, as well as a number of sample maps, can be accessed through the World Wide Web (http://www.ncgr.org/sigma).