Introduction to the Workshop
URLs Provided by Attendees
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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.
Software Tools in Support of Physical Mapping efforts at LANL
The following software tools have been developed to support physical mapping efforts at Los Alamos National Laboratory, Center for Human Genome Studies:
GRAM (Genomic Restriction map AsseMbly)
Soderlund, C., and L. P. MacGavran.
GRAM provides a visualization interface for the alignment of fingerprinted restriction fragments in cosmid clone contigs. GRAM employs a clustering algorithm to merge RFs to a set of unique fragments, and a shuffling algorithm to assemble these fragments into a permutation consistent with the RF content of and implied RF adjacency for the clones of a contig.
MAP depicts contigs of pairwise overlapping clones as an undirected graph and allows the user to edit these depictions. Using interval graph algorithms, MAP highlights forbidden structures in a graph and gives suggestions for repairs. MAP is fully integrated with the Chromosome 16 Physical Map database.
SIGMA (System for Integrated Map Assembly)
Cinkosky, M. J., M. A. Bridgers, W. M. Barber, C. D. Troup, M. Ijadi and J. W. Fickett
X Window-based software tool for creating, editing and viewing integrated genome maps. Combines data from physical, cytogenetic and linkage maps in a single, unified map. (See separate SIGMA abstract and posted Chromosome 16 Physical Map )
Chromosome 16 Map Browser
Sutherland, R. D.
Map Browser is a point-and-click front-end to the LANL Chromosome 16 database. It presents chromosome 16 breakpoint intervals and all DNA segments lying between them, organized by type. Selecting a segment expands it to provide appropriate detail: Contig membership, YAC hits, breakpoint localization, PCR primers, positioning relations, source data, fingerprint data, gel images, etc.
Beauheim, C., Pecherer, R. M., and Kelly, P.
A software package developed for interpreting hybridization autorads from high-density grids, gridHyb is used to improve the quality of existing maps, and also in the distribution of Chromosome Library clones based on probe data.
These tools will be demonstrated during the Workshop.