Unified Display of Physical Maps from AtDB

Sue Rhee rhee at genome.stanford.edu
Wed Mar 3 20:34:39 EST 1999


AtDB is pleased to announce a new version of the Unified Display of
Physical Maps. This display is designed to facilitate map-based
cloning by displaying graphically the physical maps from many groups
and methods in one site. This display can be found in AtDB's Maps page:

	http://genome-www.stanford.edu/Arabidopsis/maps.html

Or directly reached from:

	http://genome-www4.stanford.edu:8300/cgi-bin/Pchrom

Currently, the display contains BAC tiling paths from Altmann's group,
YAC tiling paths from INRA and Goodman's group, physical maps from
Schmidt and Dean's groups, Kazusa and CSHL, sequence maps from ESSA
and TIGR, and chromsomal walks from various groups.  The display
contains 10,185 unique clones (8,421 BACs, 927 YACs, 645 P1s, 149
TACs, and 70 Cosmids) and 3443 unique probes (BAC Ends, YAC Ends,
ESTs, Cloned Genes, and genetic markers). Of the probes, 550 are
genetic markers (435 RFLPs, 78 CAPS, and 37 SSLPs).

The map position of all clones and probes can be searched and graphically
displayed. Other interactive features of this display include
hide/display functions for different groups' contigs, hide/display
functions of the number of clones from Altmann group's contigs, zoom
in/out functions, and JavaScript boxes for displaying hybridization
information.

All clones and probes in the display are hot-linked. We are in the final
stages of loading the relevant information for all displayed clones and
probes into the database. At present, AGI clones displayed in this map are
not current. An updated version that includes all the sequenced clones
will be available soon.

The software for the storage and display was created by Dr. Shuai Weng
and represents the most complex display program yet written at
AtDB. More information about the display can be found in:

	http://genome-www.stanford.edu/Arabidopsis/help_physmap.html

and in NAR (1999) 27(1):79-84.

We are grateful for the following colleagues for providing data, in
some cases before publication, and helpful discussions:

T. Altmann, T. Arioli, A. Bachmair, M. Bevan, D. Bouchez, R. Buell,
K. Century, R. Chapple, C. Dean, M. Dhan, P. Dunn, R. Finkelstein,
C. Hardtke, K. Hicks, Y. Levy, O. Leyser, X. Lin, W. Lukowitz,
M. Marra, R. Martienssen, T. Mozo, L. Parnell, S. Rounsley, H. Sakai,
R. Schmidt, M. Sekhon, W. Soppe, S. Tabata, and I. Wilson

AtDB's Homepage: http://genome-www.stanford.edu/Arabidopsis/
Please send comments to atdb-curator at genome.stanford.edu

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Sue Rhee	                 rhee at genome.stanford.edu
AtDB Curator			 http://genome-www.stanford.edu/
Dept. of Genetics                FAX: +1-650-723 7016
School of Medicine               Tel: +1-650-498-6004
Stanford University
Stanford
CA 94305-5120
U.S.A.
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