Please forgive the cross-postings.
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S I G M A
System for Integrated
Genome Map Assembly
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Version 1.02 Available by FTP
SIGMA/OS -- runs with ObjectStore DBMS
SIGMA/ASCII -- runs without a DBMS
Sample human and yeast maps available
We are pleased to announce that SIGMA version 1.02 is now available by
anonymous ftp. SIGMA (System for Integrated Genome Map Assembly) is an
X-Windows, OpenLook, graphical genome map editor with the following
major features:
- Graphical, mouse-based genome map editing;
- Supports integration of data from many different types of
physical and linkage experiments;
- Enables integration of data at all appropriate levels of
resolution, from banded ideograms to restriction fragments;
- Supports creation of multiple "views" on a single map;
- Allows users to create new classes of map objects on demand;
- Supports workgroup map-building through the use of
client-server DBMS technology (SIGMA/OS version only; see
below).
In addition, SIGMA enables users to store the data on which a map is
based as a part of the map itself. Thus SIGMA:
- Keeps the underlying data as part of the map, allowing users
to know the real support for any given map;
- Automatically evaluates the map against the underlying data,
pointing out places where the two disagree;
- Creates a platform for automatic map assembly algorithms
being developed by many groups worldwide.
SIGMA is available as Sun SparcStation executable in two configurations:
- SIGMA/OS, which uses the ObjectStore, OODBMS from Object
Design, Inc. (a license from ODI is required to use this
version);
- SIGMA/ASCII, which runs without a DBMS by storing maps in
ASCII text files (no license is required to run this version).
As well, a number of sample map files in SIGMA format are available for
ftp along with the software, including:
- human maps imported from the Genome Data Base (GDB) at Johns
Hopkins University (thanks to the staff there for giving us
access to their development server);
- yeast restriction maps from ATCC (thanks to them for supplying
us with the data).
Instructions for ftp'ing and installing the files can be retrieved by
sending email containing only the text "sigma-info" (without the
quotation marks) to bioserve at t10.lanl.gov.
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This work was funded through the Los Alamos Center for Human Genome
Studies by the Office of Health and Environmental Research of DOE.
For more information on SIGMA, send email containing only the text
"sigma-info" (without the quotation marks) to bioserve at t10.lanl.gov, or
write to sigma at t10.lanl.gov, or call Michael Cinkosky at (505)
665-0840.
