Glossary

Hybridization contigs -  Thomas Altmann's group has performed a series of
hybridizations to  many Arabidopsis BAC clones.  A very large set of probes
was used; many of these probes were derived from the ends of inserts in
the BACs themselves.  By identifying BAC clones that hybridize to the same
probes, the clones were assembled into approximately 20 contigs that span
most of the genome.  For more information, see
http://www.mpimp-golm.mpg.de/101/igf_bac_cont.html.

Fingerprint contigs -  Marco Marra and colleagues at Washington University
performed restriction digests on a very large number of Arabidopsis BAC
clones.  Using the program "fpc" developed by the Sanger Center, the
restriction patterns were used to assemble the clones into overlapping
sets.  For more information, see
http://genome.wustl.edu/gsc/arab/atdatabase.shtml

Tiling path - a contiguous set of clones that completely spans a genomic
region, ideally with a minimum amount of overlap.  The genome sequencing
labs are working toward identifying a set of clones that will constitute a
minimum tiling path of the genome and serve as material for genomic
sequencing.

Size of sequence gaps -  This estimate is based primarily on analyzing the
Washington University fingerprint contigs and the Thomas Altmann
hybridization contigs.  When such estimates are performed on sequenced
regions, they typically have an accuracy of +/- 30%.

RI map -  The Recombinant Inbred map is maintained by Mary Anderson at the
Nottingham Arabidopsis Stock Center.  It is based on the set of Landsberg
and Columbia recombinant inbred lines generated by Lister and Dean.
Briefly, hundreds of molecular markers have been scored on a subset of the
RI lines; the program "Mapmaker" is used to assemble this data into a "most
likely" order.  Because Mapmaker displays the location with the most likely
probability, in some cases the predicted order may be different than the
actual order as determined by DNA sequencing.

Meinke map -  This map is maintained by David Meinke at Oklahoma State
University.  It compiles data from crosses between mutants with phenotypic
differences.  Because this map often reports assortment of markers in
plants of the same ecotype (i.e. Landsberg x Landsberg), the  map distances
on the visible map are often different from those on the RI  map.

Molecular markers - These are the set of DNA-based genetic  markers that
differ between Arabidopsis ecotypes, primarily between the strains
Landsberg and Columbia.  There are many types of molecular markers:  the
earliest are RFLPs (restriction fragment length polymorphisms), and more
recent types includes CAPS (co-dominant amplified polymorphic sites) and
SSLPs (simple sequence length polymorphisms).

Visible markers - These are genetic markers that are obvious from
examining a plant's phenotype.  They include visible mutations or
phenotypic differences between ecotypes.

BAC filters - The Arabidopsis Stock Center distributes high-density arrays
of BAC clones on nylon filters suitable for performing numerous DNA
hybridization experiments.

Sequencing Labs -